Package evaluation to test VCFTools on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T16:42:23.986 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.2s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.8 [4c63d2b9] + StatsFuns v1.5.2 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 5.51s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 1138.8 ms ✓ BGZFStreams 4669.9 ms ✓ HypothesisTests [ Info: Compiling VCF parser... 19732.2 ms ✓ VariantCallFormat 7488.2 ms ✓ VCFTools 4 dependencies successfully precompiled in 37 seconds. 66 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 47.89s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_yx7loJ/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.8 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_yx7loJ/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [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 v0.11.36 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.8 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+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 [b27032c2] LibCURL v1.0.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [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 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [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 v8.17.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 8.4s Test Summary: | Pass Total Time openvcf | 4 4 2.9s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.5s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.4s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:33:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 14.704815 seconds (10.07 M allocations: 565.809 MiB, 5.04% gc time, 93.01% compilation time: 19% of which was recompilation) 0.422727 seconds (2.40 M allocations: 143.649 MiB, 6.41% gc time, 21.77% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:31:37 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.263295 seconds (4.03 M allocations: 238.273 MiB, 1.82% gc time, 87.18% compilation time) 0.417010 seconds (2.38 M allocations: 143.410 MiB, 5.12% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 22.4s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.8s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 1.9s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.1s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:37 Progress: 0%|▏ | ETA: 0:17:26 Progress: 0%|▏ | ETA: 0:17:07 Progress: 0%|▏ | ETA: 0:16:52 Progress: 1%|▎ | ETA: 0:15:56 Progress: 1%|▎ | ETA: 0:15:30 Progress: 1%|▍ | ETA: 0:14:44 Progress: 1%|▍ | ETA: 0:14:13 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Progress: 10%|████▏ | ETA: 0:14:32 Progress: 10%|████▏ | ETA: 0:14:30 Progress: 10%|████▎ | ETA: 0:14:30 Progress: 100%|█████████████████████████████████████████| Time: 0:01:40 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:45:25 Progress: 21%|████████▋ | ETA: 0:06:20 Progress: 42%|█████████████████▎ | ETA: 0:02:21 Progress: 63%|█████████████████████████▉ | ETA: 0:01:00 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: 0 records are matched 215.163438 seconds (2.01 G allocations: 106.120 GiB, 5.88% gc time, 0.42% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 10m52.1s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:19:53 Progress: 19%|███████▉ | ETA: 0:07:13 Progress: 39%|████████████████▏ | ETA: 0:02:42 Progress: 61%|█████████████████████████▏ | ETA: 0:01:06 Progress: 84%|██████████████████████████████████▍ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 833 records are matched 118.079128 seconds (1.02 G allocations: 53.885 GiB, 5.45% gc time, 0.53% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:59:37 Progress: 21%|████████▌ | ETA: 0:06:30 Progress: 42%|█████████████████▍ | ETA: 0:02:19 Progress: 65%|██████████████████████████▋ | ETA: 0:00:56 Progress: 89%|████████████████████████████████████▍ | ETA: 0:00:13 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 493 records are matched 116.002283 seconds (1.02 G allocations: 53.885 GiB, 5.50% gc time, 0.51% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:32:03 Progress: 21%|████████▊ | ETA: 0:06:08 Progress: 44%|█████████████████▉ | ETA: 0:02:11 Progress: 66%|███████████████████████████▎ | ETA: 0:00:51 Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:01:42 [ Info: 0 records are matched 113.166166 seconds (1.02 G allocations: 53.885 GiB, 5.57% gc time, 0.50% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m49.4s 1.137226 seconds (1.27 M allocations: 68.063 MiB, 4.44% gc time, 80.54% compilation time) 0.941802 seconds (1.15 M allocations: 64.058 MiB, 80.46% compilation time) 0.971206 seconds (1.15 M allocations: 63.082 MiB, 3.39% gc time, 78.56% compilation time) 0.401853 seconds (205.72 k allocations: 10.701 MiB, 99.96% compilation time) 0.011003 seconds (6.49 k allocations: 394.992 KiB, 96.75% compilation time) 0.009320 seconds (2.65 k allocations: 165.383 KiB, 96.60% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.2s 0.880846 seconds (977.49 k allocations: 54.488 MiB, 81.82% compilation time) 0.837090 seconds (878.92 k allocations: 51.575 MiB, 4.31% gc time, 79.77% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.2s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.101967 seconds (525.76 k allocations: 30.690 MiB, 33.62% compilation time) 0.657287 seconds (645.57 k allocations: 37.293 MiB, 89.31% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:72 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:176 0.059358 seconds (520.58 k allocations: 32.160 MiB) 0.545653 seconds (595.93 k allocations: 36.386 MiB, 3.25% gc time, 84.83% compilation time) ┌ Warning: Reached end of record! Columns 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:414 ┌ Warning: Reached end of record! Rows 1357-1400 are filled with 0.0s and are NOT haplotypes! └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:501 0.202797 seconds (1.56 M allocations: 62.080 MiB, 40.73% gc time, 4.59% compilation time) 0.582773 seconds (1.71 M allocations: 70.264 MiB, 81.02% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:672 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:787 Test Summary: | Pass Total Time convert to transpose functions | 13 13 7.1s Test Summary: | Pass Total Time record info | 14 14 5.1s Test Summary: | Pass Total Time write VCF | 3 3 4.3s 2.178153 seconds (4.80 M allocations: 296.313 MiB, 4.97% gc time, 57.70% compilation time) 0.997589 seconds (2.39 M allocations: 142.635 MiB, 3.84% gc time, 22.82% compilation time) 0.944828 seconds (4.42 M allocations: 276.270 MiB, 5.54% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.0s 0.958483 seconds (605.37 k allocations: 33.378 MiB, 1.64% gc time, 45.04% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.6s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▏ | ETA: 0:18:33 Progress: 1%|▍ | ETA: 0:18:25 Progress: 1%|▌ | ETA: 0:18:35 Progress: 2%|▊ | ETA: 0:18:25 Progress: 2%|▉ | ETA: 0:18:17 Progress: 3%|█▏ | ETA: 0:18:19 Progress: 3%|█▎ | ETA: 0:18:19 Progress: 4%|█▌ | ETA: 0:18:11 Progress: 4%|█▋ | ETA: 0:17:59 Progress: 5%|█▉ | ETA: 0:17:55 Progress: 5%|██ | ETA: 0:17:55 Progress: 5%|██▎ | ETA: 0:17:39 Progress: 6%|██▌ | ETA: 0:17:24 Progress: 6%|██▋ | ETA: 0:17:19 Progress: 7%|██▉ | ETA: 0:17:15 Progress: 7%|███ | ETA: 0:17:11 Progress: 8%|███▎ | ETA: 0:17:08 Progress: 8%|███▍ | ETA: 0:17:05 Progress: 9%|███▌ | ETA: 0:17:00 Progress: 9%|███▊ | ETA: 0:16:58 Progress: 10%|███▉ | ETA: 0:16:54 Progress: 10%|████▏ | ETA: 0:16:52 Progress: 10%|████▎ | ETA: 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| ETA: 0:00:51 Progress: 96%|███████████████████████████████████████▍ | ETA: 0:00:47 Progress: 96%|███████████████████████████████████████▌ | ETA: 0:00:41 Progress: 97%|███████████████████████████████████████▋ | ETA: 0:00:36 Progress: 97%|███████████████████████████████████████▉ | ETA: 0:00:31 Progress: 98%|████████████████████████████████████████ | ETA: 0:00:26 Progress: 98%|████████████████████████████████████████▎| ETA: 0:00:22 Progress: 99%|████████████████████████████████████████▍| ETA: 0:00:17 Progress: 99%|████████████████████████████████████████▋| ETA: 0:00:12 Progress: 99%|████████████████████████████████████████▊| ETA: 0:00:07 Progress: 99%|█████████████████████████████████████████| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:18:54 Test Summary: | Pass Total Time AIM selection | 4 4 19m37.2s Test Summary: | Pass Total Time grm | 11 11 12.7s Testing VCFTools tests passed Testing completed after 2302.76s PkgEval succeeded after 2403.37s