Package evaluation of VCFTools on Julia 1.13.0-DEV.1216 (bcb9a929e5*) started at 2025-09-30T18:03:28.829 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.05s ################################################################################ # 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 4.82s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 86.12s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_mgj1xp/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_mgj1xp/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 v4.18.0 [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... Precompiling packages... 96141.5 ms ✓ DataFrames 1 dependency successfully precompiled in 97 seconds. 35 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 3.3s Test Summary: | Pass Total Time openvcf | 4 4 2.7s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.7s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.6s ┌ 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: 0:36:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 15.976544 seconds (10.93 M allocations: 683.952 MiB, 4.87% gc time, 96.37% compilation time: 22% of which was recompilation) 0.536246 seconds (2.87 M allocations: 195.945 MiB, 19.87% gc time, 18.42% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:35:04 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.593404 seconds (4.57 M allocations: 310.665 MiB, 2.31% gc time, 87.68% compilation time) 0.458379 seconds (2.85 M allocations: 195.426 MiB, 7.36% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 25.0s 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: 0:15:19 Progress: 0%|▏ | ETA: 0:14:30 Progress: 0%|▏ | ETA: 0:13:57 Progress: 1%|▎ | ETA: 0:13:21 Progress: 1%|▎ | ETA: 0:13:01 Progress: 1%|▍ | ETA: 0:12:47 Progress: 1%|▍ | ETA: 0:12:39 Progress: 1%|▌ | ETA: 0:12:45 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Progress: 10%|████ | ETA: 0:11:19 Progress: 10%|████▏ | ETA: 0:11:18 Progress: 10%|████▏ | ETA: 0:11:16 Progress: 10%|████▎ | ETA: 0:11:15 Progress: 100%|█████████████████████████████████████████| Time: 0:01:17 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 15:29:25 Progress: 19%|███████▋ | ETA: 0:06:07 Progress: 38%|███████████████▌ | ETA: 0:02:19 Progress: 58%|███████████████████████▉ | ETA: 0:01:01 Progress: 79%|████████████████████████████████▎ | ETA: 0:00:23 Progress: 99%|████████████████████████████████████████▉| ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:01:27 [ Info: 823 records are matched 174.387347 seconds (2.19 G allocations: 143.745 GiB, 8.13% gc time, 0.74% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:13 Progress: 0%|▏ | ETA: 0:18:06 Progress: 0%|▏ | ETA: 0:17:50 Progress: 0%|▏ | ETA: 0:17:51 Progress: 0%|▎ | ETA: 0:17:52 Progress: 1%|▎ | ETA: 0:17:47 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10%|████▏ | ETA: 0:15:28 Progress: 10%|████▏ | ETA: 0:15:27 Progress: 10%|████▎ | ETA: 0:15:26 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:26:29 Progress: 20%|████████▏ | ETA: 0:07:02 Progress: 40%|████████████████▌ | ETA: 0:02:37 Progress: 61%|█████████████████████████▏ | ETA: 0:01:08 Progress: 83%|██████████████████████████████████▎ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: 0 records are matched 225.313587 seconds (2.19 G allocations: 143.725 GiB, 7.06% gc time, 0.40% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 10m38.9s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:33:10 Progress: 20%|████████▏ | ETA: 0:07:04 Progress: 41%|████████████████▊ | ETA: 0:02:33 Progress: 62%|█████████████████████████▎ | ETA: 0:01:06 Progress: 85%|██████████████████████████████████▋ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: 833 records are matched 118.969785 seconds (1.11 G allocations: 72.817 GiB, 6.23% gc time, 0.53% compilation time: <1% of which was recompilation) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:22:24 Progress: 20%|████████▏ | ETA: 0:07:00 Progress: 41%|████████████████▊ | ETA: 0:02:32 Progress: 62%|█████████████████████████▌ | ETA: 0:01:04 Progress: 85%|███████████████████████████████████ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 493 records are matched 117.747421 seconds (1.11 G allocations: 72.816 GiB, 5.72% gc time, 0.49% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:27:39 Progress: 21%|████████▍ | ETA: 0:06:23 Progress: 41%|████████████████▉ | ETA: 0:02:22 Progress: 63%|██████████████████████████ | ETA: 0:00:59 Progress: 87%|███████████████████████████████████▌ | ETA: 0:00:16 Progress: 100%|█████████████████████████████████████████| Time: 0:01:42 [ Info: 0 records are matched 112.981075 seconds (1.11 G allocations: 72.816 GiB, 5.71% gc time, 0.53% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m51.9s 1.171116 seconds (1.29 M allocations: 91.609 MiB, 4.75% gc time, 84.87% compilation time) 1.042070 seconds (1.19 M allocations: 87.862 MiB, 3.27% gc time, 76.04% compilation time) 0.944814 seconds (1.19 M allocations: 86.901 MiB, 2.14% gc time, 79.22% compilation time) 0.408903 seconds (211.13 k allocations: 11.871 MiB, 99.95% compilation time) 0.011933 seconds (6.28 k allocations: 485.602 KiB, 96.35% compilation time) 0.009992 seconds (2.65 k allocations: 247.695 KiB, 96.02% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.6s 0.958326 seconds (973.49 k allocations: 75.485 MiB, 3.48% gc time, 77.87% compilation time) 0.874897 seconds (876.47 k allocations: 72.278 MiB, 6.70% gc time, 71.45% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.6s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.120439 seconds (525.34 k allocations: 50.449 MiB, 11.52% gc time, 30.30% compilation time) 0.689467 seconds (650.70 k allocations: 57.858 MiB, 1.86% gc time, 87.63% 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 0.077869 seconds (520.43 k allocations: 51.916 MiB, 12.13% gc time) 0.542203 seconds (593.98 k allocations: 56.208 MiB, 2.05% gc time, 85.17% 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 0.132942 seconds (1.56 M allocations: 81.839 MiB, 10.40% gc time, 7.06% compilation time) 0.662749 seconds (1.70 M allocations: 90.492 MiB, 12.46% gc time, 69.96% 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 7.2s Test Summary: | Pass Total Time record info | 14 14 5.1s Test Summary: | Pass Total Time write VCF | 3 3 4.6s 2.227508 seconds (5.30 M allocations: 380.878 MiB, 2.94% gc time, 55.88% compilation time) 1.019028 seconds (2.86 M allocations: 194.795 MiB, 3.78% gc time, 22.88% compilation time) 0.970646 seconds (4.89 M allocations: 358.188 MiB, 6.25% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.2s 1.058182 seconds (618.17 k allocations: 54.343 MiB, 1.42% gc time, 48.55% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.0s Test Summary: | Pass Total Time filter_chr | 4 4 2.2s Progress: 0%|▏ | ETA: 0:24:11 Progress: 1%|▎ | ETA: 0:21:51 Progress: 1%|▌ | ETA: 0:21:18 Progress: 2%|▋ | ETA: 0:21:00 Progress: 2%|▉ | ETA: 0:20:41 Progress: 2%|█ | ETA: 0:20:36 Progress: 3%|█▏ | ETA: 0:20:29 Progress: 3%|█▍ | ETA: 0:20:23 Progress: 4%|█▌ | ETA: 0:20:17 Progress: 4%|█▋ | ETA: 0:20:10 Progress: 4%|█▊ | ETA: 0:20:07 Progress: 5%|██ | ETA: 0:20:01 Progress: 5%|██▏ | ETA: 0:19:55 Progress: 6%|██▎ | ETA: 0:19:47 Progress: 6%|██▌ | ETA: 0:19:41 Progress: 6%|██▋ | ETA: 0:19:36 Progress: 7%|██▊ | ETA: 0:19:31 Progress: 7%|███ | ETA: 0:19:27 Progress: 8%|███▏ | ETA: 0:19:23 Progress: 8%|███▎ | ETA: 0:19:17 Progress: 8%|███▌ | ETA: 0:19:11 Progress: 9%|███▋ | ETA: 0:19:01 Progress: 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