Package evaluation of VCFTools on Julia 1.13.0-DEV.704 (4632cd28b9*) started at 2025-06-05T17:56:02.397 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.24s ################################################################################ # 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 v0.8.4 [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 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.4 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [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 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.7 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 [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 v1.12.0 [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 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 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 4.11s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 35.1s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_sXvPIK/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.10.4 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.5 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_sXvPIK/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 ⌅ [67c07d97] Automa v0.8.4 [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 v4.16.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.5.8 [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 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.4 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.3 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [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 v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.7 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [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 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [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 v1.12.0 [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 [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 [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 [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 [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 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.8s Test Summary: | Pass Total Time openvcf | 4 4 2.2s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.4s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.4s ┌ 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: 0:26:26 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 14.977021 seconds (11.16 M allocations: 683.756 MiB, 4.32% gc time, 92.14% compilation time: 20% of which was recompilation) 1.216967 seconds (2.87 M allocations: 195.676 MiB, 4.59% gc time, 7.11% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:23:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 3.240295 seconds (4.42 M allocations: 299.781 MiB, 2.28% gc time, 65.96% compilation time) 1.126264 seconds (2.85 M allocations: 195.466 MiB, 2.24% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 24.4s Test Summary: | Pass Total Time get sampleID | 4 4 0.0s 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 2.0s 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 6.1s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:59 Progress: 0%|▏ | ETA: 0:17:47 Progress: 0%|▏ | ETA: 0:17:41 Progress: 0%|▏ | ETA: 0:17:38 Progress: 0%|▎ | ETA: 0:17:33 Progress: 1%|▎ | ETA: 0:17:29 Progress: 1%|▎ | ETA: 0:17:27 Progress: 1%|▍ | ETA: 0:17:23 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Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:25:40 Progress: 20%|████████▏ | ETA: 0:07:05 Progress: 40%|████████████████▎ | ETA: 0:02:40 Progress: 61%|█████████████████████████ | ETA: 0:01:08 Progress: 83%|██████████████████████████████████▎ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: 488 records are matched 225.996495 seconds (2.19 G allocations: 143.727 GiB, 6.26% gc time, 0.38% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:22 Progress: 0%|▏ | ETA: 0:17:54 Progress: 0%|▏ | ETA: 0:17:44 Progress: 0%|▏ | ETA: 0:17:36 Progress: 0%|▎ | ETA: 0:17:28 Progress: 1%|▎ | ETA: 0:17:21 Progress: 1%|▎ | ETA: 0:17:16 Progress: 1%|▍ | ETA: 0:17:11 Progress: 1%|▍ | ETA: 0:17:09 Progress: 1%|▍ | ETA: 0:17:07 Progress: 1%|▍ | ETA: 0:17:05 Progress: 1%|▌ | ETA: 0:17:02 Progress: 1%|▌ | ETA: 0:17:00 Progress: 1%|▌ | ETA: 0:16:56 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Progress: 0%| | ETA: 19:19:05 Progress: 21%|████████▍ | ETA: 0:06:40 Progress: 42%|█████████████████▎ | ETA: 0:02:24 Progress: 64%|██████████████████████████▎ | ETA: 0:01:00 Progress: 87%|███████████████████████████████████▌ | ETA: 0:00:17 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 0 records are matched 224.320710 seconds (2.19 G allocations: 143.728 GiB, 6.29% gc time, 0.39% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m25.8s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:15:56 Progress: 20%|████████▏ | ETA: 0:07:02 Progress: 40%|████████████████▎ | ETA: 0:02:39 Progress: 62%|█████████████████████████▍ | ETA: 0:01:05 Progress: 85%|██████████████████████████████████▉ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 833 records are matched 118.151777 seconds (1.11 G allocations: 72.817 GiB, 6.15% gc time, 0.46% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:14:48 Progress: 21%|████████▌ | ETA: 0:06:34 Progress: 43%|█████████████████▌ | ETA: 0:02:21 Progress: 65%|██████████████████████████▌ | ETA: 0:00:57 Progress: 88%|████████████████████████████████████▏ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 493 records are matched 117.882818 seconds (1.11 G allocations: 72.816 GiB, 6.05% gc time, 0.47% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:16:49 Progress: 21%|████████▌ | ETA: 0:06:38 Progress: 42%|█████████████████▍ | ETA: 0:02:22 Progress: 66%|███████████████████████████▎ | ETA: 0:00:53 Progress: 91%|█████████████████████████████████████▏ | ETA: 0:00:11 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 0 records are matched 117.890622 seconds (1.11 G allocations: 72.817 GiB, 6.13% gc time, 0.47% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m56.1s 1.118597 seconds (1.34 M allocations: 92.915 MiB, 4.81% gc time, 89.33% compilation time) 0.963743 seconds (1.21 M allocations: 87.989 MiB, 4.84% gc time, 78.31% compilation time) 0.845634 seconds (1.22 M allocations: 87.252 MiB, 85.82% compilation time) 0.435819 seconds (216.38 k allocations: 11.788 MiB, 5.33% gc time, 99.96% compilation time) 0.009872 seconds (6.30 k allocations: 485.211 KiB, 95.92% compilation time) 0.008628 seconds (2.66 k allocations: 248.211 KiB, 96.38% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.1s 0.905083 seconds (990.22 k allocations: 75.449 MiB, 3.66% gc time, 83.63% compilation time) 0.780770 seconds (891.43 k allocations: 72.242 MiB, 2.72% gc time, 82.90% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.9s Test Summary: | Pass Total Time convert_ds | 5 5 1.4s 0.137021 seconds (525.76 k allocations: 50.464 MiB, 23.98% compilation time) 0.726889 seconds (659.65 k allocations: 57.989 MiB, 6.70% gc time, 79.30% 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 0.092997 seconds (520.43 k allocations: 51.916 MiB, 20.03% gc time) 0.482260 seconds (595.43 k allocations: 56.142 MiB, 86.78% 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 0.130628 seconds (1.56 M allocations: 81.839 MiB, 11.72% gc time, 6.41% compilation time) 0.579442 seconds (1.71 M allocations: 90.585 MiB, 3.04% gc time, 78.29% 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 8.4s Test Summary: | Pass Total Time write VCF | 3 3 5.3s 3.672285 seconds (5.28 M allocations: 379.435 MiB, 2.36% gc time, 31.83% compilation time) 1.932861 seconds (2.86 M allocations: 194.958 MiB, 2.21% gc time, 9.88% compilation time) 1.644552 seconds (4.89 M allocations: 358.250 MiB, 3.77% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 9.7s 1.670318 seconds (626.98 k allocations: 54.530 MiB, 0.95% gc time, 27.91% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.5s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▏ | ETA: 0:22:48 Progress: 1%|▍ | ETA: 0:21:01 Progress: 1%|▌ | ETA: 0:20:38 Progress: 2%|▋ | ETA: 0:20:19 Progress: 2%|▉ | ETA: 0:20:03 Progress: 2%|█ | ETA: 0:19:57 Progress: 3%|█▏ | ETA: 0:19:51 Progress: 3%|█▍ | ETA: 0:19:46 Progress: 4%|█▌ | ETA: 0:19:40 Progress: 4%|█▊ | ETA: 0:19:34 Progress: 5%|█▉ | ETA: 0:19:25 Progress: 5%|██ | ETA: 0:19:19 Progress: 5%|██▎ | ETA: 0:19:12 Progress: 6%|██▍ | ETA: 0:19:04 Progress: 6%|██▌ | ETA: 0:18:57 Progress: 7%|██▊ | ETA: 0:18:50 Progress: 7%|██▉ | ETA: 0:18:46 Progress: 7%|███▏ | ETA: 0:18:42 Progress: 8%|███▎ | ETA: 0:18:38 Progress: 8%|███▍ | ETA: 0:18:32 Progress: 9%|███▋ | ETA: 0:18:26 Progress: 9%|███▊ | ETA: 0:18:22 Progress: 10%|███▉ 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