Package evaluation of MendelPlots on Julia 1.13.0-DEV.791 (d5209bd37d*) started at 2025-07-04T18:13:19.901 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.1s ################################################################################ # Installation # Installing MendelPlots... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [7ab2ea78] + MendelPlots v0.1.6 Updating `~/.julia/environments/v1.13/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [13072b0f] + AxisAlgorithms v1.1.0 [159f3aea] + Cairo v1.1.1 [324d7699] + CategoricalArrays v0.10.8 [d360d2e6] + ChainRulesCore v1.25.2 [944b1d66] + CodecZlib v0.7.8 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌅ [5ae59095] + Colors v0.12.11 [34da2185] + Compat v4.17.0 [a81c6b42] + Compose v0.9.6 [187b0558] + ConstructionBase v1.6.0 [d38c429a] + Contour v0.6.3 [7ad07ef1] + CoupledFields v0.3.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [497a8b3b] + DoubleFloats v1.4.3 [7a1cc6ca] + FFTW v1.9.0 [1a297f60] + FillArrays v1.13.0 [53c48c17] + FixedPointNumbers v0.8.5 [c91e804a] + Gadfly v1.4.1 [14197337] + GenericLinearAlgebra v0.3.17 [a2bd30eb] + Graphics v1.1.3 [42e2da0e] + Grisu v1.0.2 [a1b4810d] + Hexagons v0.2.0 [34004b35] + HypergeometricFunctions v0.3.28 [9b13fd28] + IndirectArrays v1.0.0 [842dd82b] + InlineStrings v1.4.4 ⌅ [a98d9a8b] + Interpolations v0.15.1 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [5ab0869b] + KernelDensity v0.6.9 [b964fa9f] + LaTeXStrings v1.4.0 ⌅ [7031d0ef] + LazyGrids v0.5.0 [4345ca2d] + Loess v0.6.4 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [442fdcdd] + Measures v0.3.2 [7ab2ea78] + MendelPlots v0.1.6 [e1d29d7a] + Missings v1.2.0 [77ba4419] + NaNMath v1.1.3 [4d1e1d77] + Nullables v1.0.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [f27b6e38] + Polynomials v4.1.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [be4d8f0f] + Quadmath v0.5.13 [c84ed2f1] + Ratios v0.4.5 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [992d4aef] + Showoff v1.0.3 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [e0df1984] + TextParse v1.0.3 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [efce3f68] + 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Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [b53b4c65] + libpng_jll v1.6.50+0 [1317d2d5] + oneTBB_jll v2022.0.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.04s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 274.52s ################################################################################ # Testing # Testing MendelPlots Status `/tmp/jl_qNX9YF/Project.toml` [159f3aea] Cairo v1.1.1 ⌅ [5ae59095] Colors v0.12.11 [a81c6b42] Compose v0.9.6 [a93c6f00] DataFrames v1.7.0 [31c24e10] Distributions v0.25.120 [c91e804a] Gadfly v1.4.1 [7ab2ea78] MendelPlots v0.1.6 [189a3867] Reexport v1.2.2 [10745b16] Statistics v1.11.1 [e0df1984] TextParse v1.0.3 [8dfed614] Test v1.11.0 Status `/tmp/jl_qNX9YF/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [13072b0f] AxisAlgorithms v1.1.0 [159f3aea] Cairo v1.1.1 [324d7699] CategoricalArrays v0.10.8 [d360d2e6] ChainRulesCore v1.25.2 [944b1d66] CodecZlib v0.7.8 ⌅ [3da002f7] ColorTypes v0.11.5 ⌅ [5ae59095] Colors v0.12.11 [34da2185] Compat v4.17.0 [a81c6b42] Compose v0.9.6 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [7ad07ef1] CoupledFields v0.3.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [497a8b3b] DoubleFloats v1.4.3 [7a1cc6ca] FFTW v1.9.0 [1a297f60] FillArrays v1.13.0 [53c48c17] FixedPointNumbers v0.8.5 [c91e804a] Gadfly v1.4.1 [14197337] GenericLinearAlgebra v0.3.17 [a2bd30eb] Graphics v1.1.3 [42e2da0e] Grisu v1.0.2 [a1b4810d] Hexagons v0.2.0 [34004b35] HypergeometricFunctions v0.3.28 [9b13fd28] IndirectArrays v1.0.0 [842dd82b] InlineStrings v1.4.4 ⌅ [a98d9a8b] Interpolations v0.15.1 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [5ab0869b] KernelDensity v0.6.9 [b964fa9f] LaTeXStrings v1.4.0 ⌅ [7031d0ef] LazyGrids v0.5.0 [4345ca2d] Loess v0.6.4 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [442fdcdd] Measures v0.3.2 [7ab2ea78] MendelPlots v0.1.6 [e1d29d7a] Missings v1.2.0 [77ba4419] NaNMath v1.1.3 [4d1e1d77] Nullables v1.0.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [f27b6e38] Polynomials v4.1.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [be4d8f0f] Quadmath v0.5.13 [c84ed2f1] Ratios v0.4.5 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [992d4aef] Showoff v1.0.3 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [e0df1984] TextParse v1.0.3 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [efce3f68] WoodburyMatrices v1.0.0 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.5+0 [2e619515] Expat_jll v2.6.5+0 [f5851436] FFTW_jll v3.3.11+0 [a3f928ae] Fontconfig_jll v2.16.0+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [b0724c58] GettextRuntime_jll v0.22.4+0 [7746bdde] Glib_jll v2.84.3+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [1d5cc7b8] IntelOpenMP_jll v2025.0.4+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [e9f186c6] Libffi_jll v3.4.7+0 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.0+0 [38a345b3] Libuuid_jll v2.41.0+0 [856f044c] MKL_jll v2025.0.1+1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [36c8627f] Pango_jll v1.56.3+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [f50d1b31] Rmath_jll v0.5.1+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [b53b4c65] libpng_jll v1.6.50+0 [1317d2d5] oneTBB_jll v2022.0.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 9267.3 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 11 seconds. 49 already precompiled. WARNING: Method definition PNG(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PNG), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition PDF(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PDF), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition PS(Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Compose.PS), Any...) in module Compose at /home/pkgeval/.julia/packages/Compose/eWKZh/src/Compose.jl:138 overwritten at /home/pkgeval/.julia/packages/Compose/eWKZh/src/cairo_backends.jl:208. 115.567766 seconds (49.29 M allocations: 2.526 GiB, 1.96% gc time, 97.77% compilation time) 4.520469 seconds (7.51 M allocations: 357.845 MiB, 3.61% gc time, 47.89% compilation time: <1% of which was recompilation) 9.303690 seconds (13.04 M allocations: 594.729 MiB, 3.96% gc time, 73.46% compilation time) Test Summary: | Pass Total Time Basic Manhattan Plots (pdf and png) | 3 3 2m11.5s No basepair information will be used as the basepair position variable was not specified properly. To use BP position info, use the `posvar` argument to specify the variable in the dataframe that uses basepairs. 5.201390 seconds (8.20 M allocations: 384.010 MiB, 4.09% gc time, 56.90% compilation time) Test Summary: | Pass Total Time Advanced Manhattan Plot | 1 1 5.2s 2.336390 seconds (6.97 M allocations: 328.287 MiB, 8.41% gc time, 5.21% compilation time) Test Summary: | Pass Total Time Advanced Manhattan Plot 2 | 1 1 2.3s 10.410886 seconds (11.01 M allocations: 543.806 MiB, 2.98% gc time, 77.77% compilation time) Test Summary: | Pass Total Time Manhattan Annotation | 1 1 10.4s 27.822960 seconds (24.87 M allocations: 1.246 GiB, 1.89% gc time, 89.56% compilation time) 3.435118 seconds (7.97 M allocations: 438.966 MiB, 14.99% gc time, 7.61% compilation time) Test Summary: | Pass Total Time Basic QQ Plots | 2 2 31.3s 10.070907 seconds (10.27 M allocations: 562.187 MiB, 10.36% gc time, 66.44% compilation time) Test Summary: | Pass Total Time Advanced QQ Plot | 1 1 10.1s Test Summary: | Pass Total Time ArgumentErrors | 5 5 0.4s Testing MendelPlots tests passed Testing completed after 336.85s PkgEval succeeded after 640.24s