Package evaluation of VCFTools on Julia 1.13.0-DEV.868 (f2a8e18a98*) started at 2025-07-17T22:31:07.240 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.3s ################################################################################ # 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 v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [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 v2.2.8 [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 ⌅ [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 v5.13.1+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 4.5s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 36.3s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_9ZwYd3/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_9ZwYd3/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 v4.17.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [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 v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.4 [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 v2.2.8 [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 v8.14.1+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 v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+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... Precompiling packages... 31029.0 ms ✓ CSV 1 dependency successfully precompiled in 32 seconds. 38 already precompiled. Precompiling packages... 30582.7 ms ✓ PrettyTables 83704.7 ms ✓ DataFrames 2 dependencies successfully precompiled in 115 seconds. 33 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 3.8s Test Summary: | Pass Total Time openvcf | 4 4 2.6s 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: 0:25:38 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 14.473847 seconds (10.58 M allocations: 663.916 MiB, 5.05% gc time, 96.20% compilation time: 21% of which was recompilation) 0.511518 seconds (2.86 M allocations: 195.669 MiB, 12.78% gc time, 16.00% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:23:20 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.452959 seconds (4.37 M allocations: 298.090 MiB, 3.02% gc time, 84.28% compilation time) 0.408611 seconds (2.85 M allocations: 195.416 MiB, 6.59% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.5s 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 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.0s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:36 Progress: 0%|▏ | ETA: 0:18:52 Progress: 0%|▏ | ETA: 0:18:21 Progress: 0%|▏ | ETA: 0:18:03 Progress: 0%|▎ | ETA: 0:17:51 Progress: 1%|▎ | ETA: 0:17:47 Progress: 1%|▎ | ETA: 0:17:40 Progress: 1%|▎ | ETA: 0:17:35 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Progress: 10%|████▎ | ETA: 0:15:24 Progress: 10%|████▎ | ETA: 0:15:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:12:23 Progress: 19%|███████▉ | ETA: 0:07:15 Progress: 39%|████████████████ | ETA: 0:02:43 Progress: 61%|████████████████████████▉ | ETA: 0:01:09 Progress: 83%|█████████████████████████████████▉ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 488 records are matched 224.017205 seconds (2.19 G allocations: 143.726 GiB, 6.54% gc time, 0.38% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:15 Progress: 0%|▏ | ETA: 0:17:53 Progress: 0%|▏ | ETA: 0:17:31 Progress: 0%|▏ | ETA: 0:17:25 Progress: 0%|▎ | ETA: 0:17:17 Progress: 1%|▎ | ETA: 0:17:07 Progress: 1%|▎ | ETA: 0:17:02 Progress: 1%|▍ | ETA: 0:17:00 Progress: 1%|▍ | ETA: 0:16:58 Progress: 1%|▍ | ETA: 0:16:59 Progress: 1%|▌ | ETA: 0:16:59 Progress: 1%|▌ | ETA: 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100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:50:40 Progress: 20%|████████▎ | ETA: 0:07:03 Progress: 40%|████████████████▋ | ETA: 0:02:39 Progress: 62%|█████████████████████████▌ | ETA: 0:01:06 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 0 records are matched 226.720206 seconds (2.19 G allocations: 143.725 GiB, 6.45% gc time, 0.37% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m26.9s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:20:06 Progress: 19%|███████▋ | ETA: 0:07:30 Progress: 39%|███████████████▉ | ETA: 0:02:47 Progress: 60%|████████████████████████▋ | ETA: 0:01:10 Progress: 81%|█████████████████████████████████▎ | ETA: 0:00:25 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 833 records are matched 118.264655 seconds (1.11 G allocations: 72.817 GiB, 6.20% gc time, 0.46% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:47:07 Progress: 20%|████████▎ | ETA: 0:07:05 Progress: 41%|████████████████▊ | ETA: 0:02:34 Progress: 63%|█████████████████████████▉ | ETA: 0:01:03 Progress: 85%|███████████████████████████████████ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 493 records are matched 120.422831 seconds (1.11 G allocations: 72.816 GiB, 6.07% gc time, 0.49% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:48:19 Progress: 21%|████████▋ | ETA: 0:06:38 Progress: 43%|█████████████████▊ | ETA: 0:02:20 Progress: 67%|███████████████████████████▍ | ETA: 0:00:54 Progress: 90%|█████████████████████████████████████▏ | ETA: 0:00:12 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 0 records are matched 120.198253 seconds (1.11 G allocations: 72.816 GiB, 6.11% gc time, 0.48% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m01.1s 1.148604 seconds (1.28 M allocations: 91.345 MiB, 4.09% gc time, 85.63% compilation time) 0.972475 seconds (1.16 M allocations: 86.632 MiB, 3.42% gc time, 80.55% compilation time) 0.873673 seconds (1.16 M allocations: 85.882 MiB, 85.75% compilation time) 0.439937 seconds (203.61 k allocations: 11.563 MiB, 5.24% gc time, 99.95% compilation time) 0.010206 seconds (6.18 k allocations: 483.492 KiB, 96.40% compilation time) 0.008548 seconds (2.65 k allocations: 247.555 KiB, 95.75% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.2s 0.924104 seconds (952.92 k allocations: 74.547 MiB, 3.59% gc time, 82.92% compilation time) 0.797398 seconds (861.52 k allocations: 71.601 MiB, 2.80% gc time, 82.50% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.6s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.157111 seconds (525.31 k allocations: 50.449 MiB, 32.11% gc time, 21.13% compilation time) 0.678120 seconds (647.53 k allocations: 57.715 MiB, 3.77% gc time, 82.91% 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 0.078151 seconds (520.43 k allocations: 51.916 MiB, 20.39% gc time) 0.537054 seconds (589.76 k allocations: 56.017 MiB, 2.54% gc time, 85.68% 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 0.140434 seconds (1.56 M allocations: 81.839 MiB, 10.75% gc time, 6.30% compilation time) 0.610575 seconds (1.70 M allocations: 90.369 MiB, 2.73% gc time, 77.74% 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 6.2s Test Summary: | Pass Total Time record info | 14 14 5.3s Test Summary: | Pass Total Time write VCF | 3 3 4.6s 2.089056 seconds (5.25 M allocations: 378.662 MiB, 4.35% gc time, 52.30% compilation time) 0.958445 seconds (2.86 M allocations: 195.106 MiB, 4.79% gc time, 21.38% compilation time) 0.914295 seconds (4.89 M allocations: 358.187 MiB, 6.46% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.5s 0.976797 seconds (618.95 k allocations: 54.418 MiB, 1.62% gc time, 48.15% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.8s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▏ | ETA: 0:23:02 Progress: 1%|▍ | ETA: 0:20:57 Progress: 1%|▌ | ETA: 0:20:37 Progress: 2%|▋ | ETA: 0:20:17 Progress: 2%|▉ | ETA: 0:19:42 Progress: 3%|█ | ETA: 0:19:43 Progress: 3%|█▎ | ETA: 0:19:40 Progress: 3%|█▍ | ETA: 0:19:43 Progress: 4%|█▌ | ETA: 0:19:38 Progress: 4%|█▊ | ETA: 0:19:36 Progress: 5%|█▉ | ETA: 0:19:31 Progress: 5%|██ | ETA: 0:19:23 Progress: 6%|██▎ | ETA: 0:18:56 Progress: 6%|██▌ | ETA: 0:18:53 Progress: 6%|██▋ | ETA: 0:18:51 Progress: 7%|██▊ | ETA: 0:18:49 Progress: 7%|███ | ETA: 0:18:46 Progress: 8%|███▏ | ETA: 0:18:44 Progress: 8%|███▎ | ETA: 0:18:40 Progress: 8%|███▌ | ETA: 0:18:36 Progress: 9%|███▋ | ETA: 0:18:32 Progress: 9%|███▊ | ETA: 0:18:28 Progress: 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