Package evaluation of HapLink on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T08:08:28.603 ################################################################################ # Set-up # Set-up completed after 0.26s ################################################################################ # Installation # Installing HapLink... Resolving package versions... Installed HapLink ─ v1.1.0 Updating `~/.julia/environments/v1.13/Project.toml` [8ca39d33] + HapLink v1.1.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 [c7e460c6] + ArgParse v1.2.0 ⌅ [67c07d97] + Automa v0.7.0 [28d598bf] + BGZFStreams v0.3.2 [00701ae9] + BioAlignments v3.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.1 [3c28c6f8] + BioSymbols v5.2.0 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.4 [863f3e99] + Comonicon v1.0.8 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [5218b696] + Configurations v0.17.6 [187b0558] + ConstructionBase v1.5.8 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [31c24e10] + Distributions v0.25.119 [ffbed154] + DocStringExtensions v0.9.4 [55351af7] + ExproniconLite v0.10.14 ⌅ [c2308a5c] + FASTX v1.3.0 ⌅ [8fc22ac5] + FilePaths v0.8.3 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 ⌅ [899a7d2d] + GenomicFeatures v2.1.0 [c27321d9] + Glob v1.3.1 [8ca39d33] + HapLink v1.1.0 [34004b35] + HypergeometricFunctions v0.3.28 ⌅ [09f84164] + HypothesisTests v0.10.13 ⌅ [4ffb77ac] + Indexes v0.1.3 [524e6230] + IntervalTrees v1.1.0 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.34 [9b87118b] + PackageCompiler v2.2.0 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [05181044] + RelocatableFolders v1.0.1 [ae029012] + Requires v1.3.1 ⌅ [79098fc4] + Rmath v0.7.1 [f2b01f46] + Roots v2.2.7 [6c6a2e73] + Scratch v1.2.1 [eef6e190] + SequenceVariation v0.2.2 [a2af1166] + SortingAlgorithms v1.2.1 ⌅ [a9a3c162] + SparseArrayKit v0.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.5.0 [69024149] + StringEncodings v0.3.7 [b718987f] + TextWrap v1.0.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [9d95972d] + TupleTools v1.6.0 [7200193e] + Twiddle v1.1.2 [28eba6e3] + VariantCallFormat v0.5.6 ⌅ [d759349c] + XAM v0.3.1 [ddb6d928] + YAML v0.4.13 [94ce4f54] + Libiconv_jll v1.18.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 ⌅ [f50d1b31] + Rmath_jll v0.4.3+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching 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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [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 [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 v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+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` Building HapLink → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/cf5533ecfe3db9cbb8df21483bc6dc863c425b4f/build.log` Installation completed after 325.18s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 7079.9 ms ✓ SparseArrayKit 2969.2 ms ✓ Automa 2517.9 ms ✓ SequenceVariation 4929.5 ms ✓ Distributions → DistributionsTestExt 23545.4 ms ✓ XAM 18692.3 ms ✓ VariantCallFormat 17394.3 ms ✓ FASTX 47240.5 ms ? HapLink 7 dependencies successfully precompiled in 126 seconds. 114 already precompiled. 1 dependencies failed but may be precompilable after restarting julia 2 dependencies had output during precompilation: ┌ HapLink │ WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(Statistics.cov), SparseArrays.SparseMatrixCSC{Tv, Ti} where Ti<:Integer where Tv) in module SparseArraysExt at /home/pkgeval/.julia/packages/Statistics/gbcbG/ext/SparseArraysExt.jl:14 overwritten in module SparseArraysExt on the same line (check for duplicate calls to `include`). │ ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. └ ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 136.02s ################################################################################ # Loading # Loading HapLink... Precompiling packages... Info Given HapLink was explicitly requested, output will be shown live  [ Info: Compiling VCF parser... 126031.4 ms ✓ HapLink 1 dependency successfully precompiled in 128 seconds. 121 already precompiled. 1 dependency had output during precompilation: ┌ HapLink │ [Output was shown above] └ Loading completed after 141.26s PkgEval succeeded after 626.9s