Package evaluation of VCFTools on Julia 1.13.0-DEV.1234 (bbaa34b41d*) started at 2025-10-01T19:09:15.352 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.32s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/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 v0.19.1 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.14.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [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 v0.11.35 [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 v0.8.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.1 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.7 [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 v0.7.0 [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 v5.13.1+0 Installation completed after 5.82s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 37.47s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_VCmZFd/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.6 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [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_VCmZFd/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 v1.8.0 [864edb3b] DataStructures v0.19.1 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [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 v0.11.35 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.0.11 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [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 v0.6.4 [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 v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [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 v8.16.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.2+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 v5.13.1+0 [8e850ede] nghttp2_jll v1.67.1+0 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 8.9s 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 3.5s ┌ 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: 0:36:48 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 15.482022 seconds (10.75 M allocations: 674.101 MiB, 4.84% gc time, 96.11% compilation time: 19% of which was recompilation) 0.468487 seconds (2.87 M allocations: 195.745 MiB, 11.61% gc time, 19.47% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:34:06 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.513906 seconds (4.57 M allocations: 310.476 MiB, 2.06% gc time, 87.29% compilation time) 0.455501 seconds (2.85 M allocations: 195.548 MiB, 6.00% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.7s 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 1.9s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.1s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.0s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.6s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:56 Progress: 0%|▏ | ETA: 0:18:35 Progress: 0%|▏ | ETA: 0:18:33 Progress: 0%|▏ | ETA: 0:18:25 Progress: 0%|▎ | ETA: 0:18:07 Progress: 1%|▎ | ETA: 0:18:03 Progress: 1%|▎ | ETA: 0:18:02 Progress: 1%|▎ | ETA: 0:18:02 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0:16:12 Progress: 10%|████ | ETA: 0:16:11 Progress: 10%|████ | ETA: 0:16:10 Progress: 10%|████ | ETA: 0:16:10 Progress: 10%|████▏ | ETA: 0:16:09 Progress: 10%|████▏ | ETA: 0:16:08 Progress: 10%|████▏ | ETA: 0:16:07 Progress: 10%|████▎ | ETA: 0:16:06 Progress: 10%|████▎ | ETA: 0:16:05 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:15:09 Progress: 20%|████████ | ETA: 0:07:28 Progress: 39%|████████████████ | ETA: 0:02:50 Progress: 61%|████████████████████████▉ | ETA: 0:01:12 Progress: 82%|█████████████████████████████████▋ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 0 records are matched 234.341143 seconds (2.19 G allocations: 143.725 GiB, 6.46% gc time, 0.38% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m45.6s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:58:33 Progress: 19%|███████▊ | ETA: 0:07:43 Progress: 38%|███████████████▊ | ETA: 0:02:53 Progress: 59%|████████████████████████▎ | ETA: 0:01:15 Progress: 80%|████████████████████████████████▋ | ETA: 0:00:28 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: 833 records are matched 121.485015 seconds (1.11 G allocations: 72.816 GiB, 6.19% gc time, 0.50% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:52:05 Progress: 20%|████████▎ | ETA: 0:07:07 Progress: 41%|████████████████▋ | ETA: 0:02:38 Progress: 62%|█████████████████████████▌ | ETA: 0:01:06 Progress: 85%|██████████████████████████████████▋ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 493 records are matched 120.535889 seconds (1.11 G allocations: 72.816 GiB, 6.21% gc time, 0.50% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:54:03 Progress: 20%|████████▏ | ETA: 0:07:10 Progress: 40%|████████████████▌ | ETA: 0:02:40 Progress: 63%|█████████████████████████▊ | ETA: 0:01:05 Progress: 85%|██████████████████████████████████▉ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 0 records are matched 120.770792 seconds (1.11 G allocations: 72.816 GiB, 6.15% gc time, 0.50% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m05.0s 1.088197 seconds (1.29 M allocations: 91.596 MiB, 4.44% gc time, 79.21% compilation time) 0.907746 seconds (1.19 M allocations: 87.923 MiB, 76.53% compilation time) 1.000657 seconds (1.19 M allocations: 86.889 MiB, 4.03% gc time, 81.85% compilation time) 0.410968 seconds (211.14 k allocations: 11.871 MiB, 99.95% compilation time) 0.010617 seconds (6.28 k allocations: 485.602 KiB, 96.57% compilation time) 0.008970 seconds (2.65 k allocations: 247.695 KiB, 95.99% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.2s 0.925800 seconds (977.00 k allocations: 75.624 MiB, 4.10% gc time, 77.21% compilation time) 0.911914 seconds (876.48 k allocations: 72.277 MiB, 7.29% gc time, 72.62% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.4s Test Summary: | Pass Total Time convert_ds | 5 5 1.5s 0.143933 seconds (525.34 k allocations: 50.449 MiB, 21.40% compilation time) 0.707298 seconds (650.69 k allocations: 57.862 MiB, 6.83% gc time, 76.47% 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 0.062946 seconds (520.43 k allocations: 51.916 MiB) 0.544476 seconds (593.99 k allocations: 56.211 MiB, 3.01% gc time, 83.93% 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 0.127841 seconds (1.56 M allocations: 81.839 MiB, 13.18% gc time, 6.38% compilation time) 0.538964 seconds (1.70 M allocations: 90.491 MiB, 3.15% gc time, 77.25% 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 6.4s Test Summary: | Pass Total Time record info | 14 14 4.9s Test Summary: | Pass Total Time write VCF | 3 3 4.3s 2.621711 seconds (5.30 M allocations: 381.194 MiB, 19.95% gc time, 45.52% compilation time) 1.032293 seconds (2.86 M allocations: 194.858 MiB, 3.95% gc time, 21.70% compilation time) 0.940218 seconds (4.89 M allocations: 358.188 MiB, 5.74% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.6s 1.049897 seconds (609.33 k allocations: 53.839 MiB, 1.37% gc time, 43.65% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.9s Test Summary: | Pass Total Time filter_chr | 4 4 1.6s Progress: 0%|▏ | ETA: 0:24:38 Progress: 1%|▎ | ETA: 0:22:17 Progress: 1%|▌ | ETA: 0:21:35 Progress: 2%|▋ | ETA: 0:21:10 Progress: 2%|▊ | ETA: 0:20:49 Progress: 2%|█ | ETA: 0:20:39 Progress: 3%|█▏ | ETA: 0:20:30 Progress: 3%|█▎ | ETA: 0:20:23 Progress: 4%|█▌ | ETA: 0:20:15 Progress: 4%|█▋ | ETA: 0:20:08 Progress: 4%|█▊ | ETA: 0:20:03 Progress: 5%|██ | ETA: 0:19:59 Progress: 5%|██▏ | ETA: 0:19:54 Progress: 6%|██▎ | ETA: 0:19:47 Progress: 6%|██▌ | ETA: 0:19:41 Progress: 6%|██▋ | ETA: 0:19:36 Progress: 7%|██▊ | ETA: 0:19:30 Progress: 7%|███ | ETA: 0:19:23 Progress: 8%|███▏ | ETA: 0:19:20 Progress: 8%|███▎ | ETA: 0:19:15 Progress: 8%|███▌ | ETA: 0:19:09 Progress: 9%|███▋ | ETA: 0:19:02 Progress: 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| Pass Total Time grm | 11 11 12.4s Testing VCFTools tests passed Testing completed after 2617.81s PkgEval succeeded after 2698.01s