Package evaluation to test VCFTools on Julia 1.14.0-DEV.1826 (44c835795b*) started at 2026-03-02T16:56:01.807 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.49s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed CommonSolve ───────────── v0.2.6 Installed DataStructures ────────── v0.19.3 Installed DelimitedFiles ────────── v1.9.1 Installed FillArrays ────────────── v1.16.0 Installed MacroTools ────────────── v0.5.16 Installed HypergeometricFunctions ─ v0.3.28 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed OrderedCollections ────── v1.8.1 Installed StatsBase ─────────────── v0.34.10 Installed TranscodingStreams ────── v0.11.3 Installed CodecZlib ─────────────── v0.7.8 Installed VCFTools ──────────────── v0.2.10 Installed SIMD ──────────────────── v3.7.2 Installed DataAPI ───────────────── v1.16.0 Installed Combinatorics ─────────── v1.1.0 Installed StatsAPI ──────────────── v1.8.0 Installed Statistics ────────────── v1.11.1 Installed ProgressMeter ─────────── v1.11.0 Installed HypothesisTests ───────── v0.11.6 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed IrrationalConstants ───── v0.2.6 Installed QuadGK ────────────────── v2.11.2 Installed PrecompileTools ───────── v1.3.3 Installed LogExpFunctions ───────── v0.3.29 Installed BufferedStreams ───────── v1.2.2 Installed Rmath ─────────────────── v0.9.0 Installed StatsFuns ─────────────── v1.5.2 Installed Roots ─────────────────── v2.2.13 Installed BioGenerics ───────────── v0.1.5 Installed Distributions ─────────── v0.25.123 Installed Reexport ──────────────── v1.2.2 Installed SpecialFunctions ──────── v2.7.1 Installed InverseFunctions ──────── v0.1.17 Installed PtrArrays ─────────────── v1.4.0 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed PDMats ────────────────── v0.11.37 Installed Automa ────────────────── v1.1.0 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed Preferences ───────────── v1.5.2 Installed BGZFStreams ───────────── v0.3.2 Installed Accessors ─────────────── v0.1.43 Installed VariantCallFormat ─────── v0.5.9 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [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 v1.1.0 [38540f10] + CommonSolve v0.2.6 [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 v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [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 v0.11.37 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.13 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [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 v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 9.57s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4510.4 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4911.6 ms ✓ MacroTools 1785.8 ms ✓ InlineStrings 846.8 ms ✓ Reexport 1200.9 ms ✓ Statistics 897.6 ms ✓ DataAPI 1292.2 ms ✓ ConstructionBase 2311.2 ms ✓ IrrationalConstants 841.7 ms ✓ DataValueInterfaces 958.4 ms ✓ StatsAPI 1357.6 ms ✓ OrderedCollections 910.9 ms ✓ InvertedIndices 1007.1 ms ✓ InverseFunctions 894.7 ms ✓ CompositionsBase 1177.1 ms ✓ DocStringExtensions 2269.1 ms ✓ Combinatorics 1070.2 ms ✓ WorkerUtilities 2270.5 ms ✓ FillArrays 1111.2 ms ✓ BufferedStreams 870.0 ms ✓ PtrArrays 823.3 ms ✓ CommonSolve 1389.0 ms ✓ TranscodingStreams 816.3 ms ✓ IteratorInterfaceExtensions 893.0 ms ✓ LaTeXStrings 2005.0 ms ✓ Crayons 1981.5 ms ✓ PDMats 1051.4 ms ✓ DelimitedFiles 1943.6 ms ✓ ProgressMeter 2185.6 ms ✓ SentinelArrays 1231.1 ms ✓ Compat 1211.9 ms ✓ Preferences 1408.6 ms ✓ Statistics → SparseArraysExt 1020.9 ms ✓ Missings 1111.1 ms ✓ PooledArrays 827.6 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3659.4 ms ✓ DataStructures 1693.2 ms ✓ InverseFunctions → InverseFunctionsTestExt 894.4 ms ✓ InverseFunctions → InverseFunctionsDatesExt 850.6 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1385.4 ms ✓ LogExpFunctions 1595.1 ms ✓ FillArrays → FillArraysSparseArraysExt 1067.7 ms ✓ FillArrays → FillArraysStatisticsExt 1012.2 ms ✓ AliasTables 970.5 ms ✓ BioGenerics 1083.4 ms ✓ CodecZlib 796.6 ms ✓ TableTraits 1542.6 ms ✓ FillArrays → FillArraysPDMatsExt 947.0 ms ✓ Compat → CompatLinearAlgebraExt 1489.0 ms ✓ JLLWrappers 955.6 ms ✓ PrecompileTools 1117.8 ms ✓ SortingAlgorithms 2434.6 ms ✓ QuadGK 5499.7 ms ✓ Accessors 900.4 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1086.8 ms ✓ BGZFStreams 1917.2 ms ✓ Tables 2249.6 ms ✓ FilePathsBase 1521.1 ms ✓ Rmath_jll 1579.6 ms ✓ OpenSpecFun_jll 3417.3 ms ✓ StringManipulation 14967.5 ms ✓ SIMD 17870.8 ms ✓ Parsers 4825.0 ms ✓ StatsBase 2581.4 ms ✓ Accessors → LinearAlgebraExt 1767.0 ms ✓ Accessors → TestExt 2997.6 ms ✓ FilePathsBase → FilePathsBaseTestExt 1033.4 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1662.0 ms ✓ Rmath 5392.7 ms ✓ SpecialFunctions 42381.1 ms ✓ PrettyTables 17713.3 ms ✓ Automa 991.2 ms ✓ InlineStrings → ParsersExt 1479.6 ms ✓ PDMats → StatsBaseExt 7173.1 ms ✓ Roots 2091.9 ms ✓ HypergeometricFunctions 84627.9 ms ✓ DataFrames [ Info: Compiling VCF parser... 16227.5 ms ✓ VariantCallFormat 2569.9 ms ✓ WeakRefStrings 3122.5 ms ✓ StatsFuns 27013.2 ms ✓ CSV 1058.2 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9461.6 ms ✓ Distributions 3631.9 ms ✓ Distributions → DistributionsTestExt 4090.9 ms ✓ HypothesisTests 4680.3 ms ✓ VCFTools 84 dependencies successfully precompiled in 371 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 404.38s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_MRDjAO/Project.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.7.1 [2913bbd2] StatsBase v0.34.10 [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_MRDjAO/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [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 v0.10.16 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.6 [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 v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [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 v0.11.37 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.2.3 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.13 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.4 [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 v1.13.0 [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 v8.18.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.5+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [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 2.9s Test Summary: | Pass Total Time openvcf | 4 4 2.8s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.5s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s 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: 0:36:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 15.220716 seconds (9.00 M allocations: 545.662 MiB, 1.31% gc time, 95.64% compilation time: 17% of which was recompilation) 0.421478 seconds (2.37 M allocations: 141.298 MiB, 11.91% gc time, 16.13% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:34:28 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 4.074561 seconds (3.92 M allocations: 238.390 MiB, 13.72% gc time, 76.37% compilation time: <1% of which was recompilation) 0.467690 seconds (2.37 M allocations: 141.243 MiB, 3.99% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.9s 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 2.0s 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 1.7s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:02 Progress: 0%|▏ | ETA: 0:17:00 Progress: 0%|▏ | ETA: 0:19:51 Progress: 0%|▏ | ETA: 0:18:53 Progress: 1%|▎ | ETA: 0:18:22 Progress: 1%|▎ | ETA: 0:17:52 Progress: 1%|▎ | ETA: 0:18:42 Progress: 1%|▍ | ETA: 0:18:37 Progress: 1%|▍ | ETA: 0:18:14 Progress: 1%|▍ | ETA: 0:17:55 Progress: 1%|▌ | ETA: 0:17:35 Progress: 1%|▌ | ETA: 0:18:05 Progress: 1%|▌ | ETA: 0:18:01 Progress: 1%|▋ | ETA: 0:17:49 Progress: 2%|▋ | ETA: 0:17:36 Progress: 2%|▋ | ETA: 0:17:28 Progress: 2%|▊ | ETA: 0:17:25 Progress: 2%|▊ | ETA: 0:17:47 Progress: 2%|▊ | ETA: 0:17:43 Progress: 2%|▉ | ETA: 0:17:37 Progress: 2%|▉ | ETA: 0:17:33 Progress: 2%|▉ | ETA: 0:17:29 Progress: 2%|█ | ETA: 0:17:43 Progress: 2%|█ | ETA: 0:17:38 Progress: 3%|█ | ETA: 0:17:31 Progress: 3%|█▏ | ETA: 0:17:27 Progress: 3%|█▏ | ETA: 0:17:23 Progress: 3%|█▏ | ETA: 0:17:19 Progress: 3%|█▎ | ETA: 0:17:33 Progress: 3%|█▎ | ETA: 0:17:29 Progress: 3%|█▎ | ETA: 0:17:25 Progress: 3%|█▍ | ETA: 0:17:22 Progress: 3%|█▍ | ETA: 0:17:20 Progress: 3%|█▍ | ETA: 0:17:30 Progress: 4%|█▌ | ETA: 0:17:28 Progress: 4%|█▌ | ETA: 0:17:25 Progress: 4%|█▌ | ETA: 0:17:22 Progress: 4%|█▋ | ETA: 0:17:18 Progress: 4%|█▋ | ETA: 0:17:13 Progress: 4%|█▋ | ETA: 0:17:24 Progress: 4%|█▊ | ETA: 0:17:21 Progress: 4%|█▊ | ETA: 0:17:17 Progress: 4%|█▊ | ETA: 0:17:15 Progress: 5%|█▉ | ETA: 0:17:12 Progress: 5%|█▉ | ETA: 0:17:18 Progress: 5%|█▉ | ETA: 0:17:18 Progress: 5%|██ | ETA: 0:17:14 Progress: 5%|██ | ETA: 0:17:11 Progress: 5%|██ | ETA: 0:17:09 Progress: 5%|██▏ | ETA: 0:17:06 Progress: 5%|██▏ | ETA: 0:17:13 Progress: 5%|██▏ | ETA: 0:17:11 Progress: 5%|██▎ | ETA: 0:17:03 Progress: 6%|██▎ | ETA: 0:16:55 Progress: 6%|██▍ | ETA: 0:16:51 Progress: 6%|██▍ | ETA: 0:16:48 Progress: 6%|██▍ | ETA: 0:16:44 Progress: 6%|██▌ | ETA: 0:16:40 Progress: 6%|██▌ | ETA: 0:16:37 Progress: 6%|██▌ | ETA: 0:16:35 Progress: 6%|██▋ | ETA: 0:16:41 Progress: 6%|██▋ | ETA: 0:16:39 Progress: 7%|██▋ | ETA: 0:16:37 Progress: 7%|██▊ | ETA: 0:16:35 Progress: 7%|██▊ | ETA: 0:16:33 Progress: 7%|██▊ | ETA: 0:16:38 Progress: 7%|██▉ | ETA: 0:16:37 Progress: 7%|██▉ | ETA: 0:16:35 Progress: 7%|██▉ | ETA: 0:16:33 Progress: 7%|███ | ETA: 0:16:30 Progress: 7%|███ | ETA: 0:16:33 Progress: 7%|███ | ETA: 0:16:33 Progress: 8%|███▏ | ETA: 0:16:31 Progress: 8%|███▏ | ETA: 0:16:28 Progress: 8%|███▏ | ETA: 0:16:27 Progress: 8%|███▎ | ETA: 0:16:24 Progress: 8%|███▎ | ETA: 0:16:29 Progress: 8%|███▎ | ETA: 0:16:28 Progress: 8%|███▍ | ETA: 0:16:26 Progress: 8%|███▍ | ETA: 0:16:23 Progress: 8%|███▍ | ETA: 0:16:21 Progress: 8%|███▌ | ETA: 0:16:24 Progress: 9%|███▌ | ETA: 0:16:22 Progress: 9%|███▌ | ETA: 0:16:19 Progress: 9%|███▋ | ETA: 0:16:16 Progress: 9%|███▋ | ETA: 0:16:14 Progress: 9%|███▋ | ETA: 0:16:12 Progress: 9%|███▊ | ETA: 0:16:15 Progress: 9%|███▊ | ETA: 0:16:14 Progress: 9%|███▊ | ETA: 0:16:12 Progress: 9%|███▉ | ETA: 0:16:10 Progress: 9%|███▉ | ETA: 0:16:09 Progress: 10%|███▉ | ETA: 0:16:11 Progress: 10%|████ | ETA: 0:16:11 Progress: 10%|████ | ETA: 0:16:09 Progress: 10%|████ | ETA: 0:16:08 Progress: 10%|████▏ | ETA: 0:16:06 Progress: 10%|████▏ | ETA: 0:16:04 Progress: 10%|████▏ | ETA: 0:16:07 Progress: 10%|████▎ | ETA: 0:16:06 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:49:44 Progress: 19%|███████▉ | ETA: 0:07:49 Progress: 39%|███████████████▉ | ETA: 0:03:00 Progress: 58%|███████████████████████▊ | ETA: 0:01:23 Progress: 78%|████████████████████████████████▏ | ETA: 0:00:32 Progress: 100%|█████████████████████████████████████████| Time: 0:01:56 [ Info: 823 records are matched 238.335210 seconds (2.01 G allocations: 106.068 GiB, 12.98% gc time, 0.60% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:07 Progress: 0%|▏ | ETA: 0:17:03 Progress: 0%|▏ | ETA: 0:16:57 Progress: 0%|▏ | ETA: 0:18:55 Progress: 0%|▎ | ETA: 0:18:48 Progress: 1%|▎ | ETA: 0:18:26 Progress: 1%|▎ | ETA: 0:18:07 Progress: 1%|▍ | ETA: 0:17:53 Progress: 1%|▍ | ETA: 0:17:46 Progress: 1%|▍ | ETA: 0:18:33 Progress: 1%|▌ | ETA: 0:18:24 Progress: 1%|▌ | ETA: 0:18:13 Progress: 1%|▌ | ETA: 0:18:04 Progress: 1%|▋ | ETA: 0:17:59 Progress: 1%|▋ | ETA: 0:18:26 Progress: 2%|▋ | ETA: 0:18:12 Progress: 2%|▊ | ETA: 0:17:49 Progress: 2%|▊ | ETA: 0:17:25 Progress: 2%|▊ | ETA: 0:17:16 Progress: 2%|▉ | ETA: 0:17:32 Progress: 2%|▉ | ETA: 0:17:29 Progress: 2%|▉ | ETA: 0:17:27 Progress: 2%|█ | ETA: 0:17:23 Progress: 2%|█ | ETA: 0:17:19 Progress: 3%|█ | ETA: 0:17:16 Progress: 3%|█▏ | ETA: 0:17:38 Progress: 3%|█▏ | ETA: 0:17:35 Progress: 3%|█▏ | ETA: 0:17:31 Progress: 3%|█▎ | ETA: 0:17:27 Progress: 3%|█▎ | ETA: 0:17:24 Progress: 3%|█▎ | ETA: 0:17:37 Progress: 3%|█▍ | ETA: 0:17:37 Progress: 3%|█▍ | ETA: 0:17:32 Progress: 3%|█▍ | ETA: 0:17:28 Progress: 4%|█▌ | ETA: 0:17:26 Progress: 4%|█▌ | ETA: 0:17:24 Progress: 4%|█▌ | ETA: 0:17:36 Progress: 4%|█▋ | ETA: 0:17:34 Progress: 4%|█▋ | ETA: 0:17:31 Progress: 4%|█▋ | ETA: 0:17:28 Progress: 4%|█▊ | ETA: 0:17:26 Progress: 4%|█▊ | ETA: 0:17:23 Progress: 4%|█▊ | ETA: 0:17:29 Progress: 4%|█▉ | ETA: 0:17:27 Progress: 5%|█▉ | ETA: 0:17:24 Progress: 5%|█▉ | ETA: 0:17:20 Progress: 5%|██ | ETA: 0:17:17 Progress: 5%|██ | ETA: 0:17:22 Progress: 5%|██ | ETA: 0:17:20 Progress: 5%|██▏ | ETA: 0:17:18 Progress: 5%|██▏ | ETA: 0:17:15 Progress: 5%|██▏ | ETA: 0:17:13 Progress: 5%|██▎ | ETA: 0:17:21 Progress: 5%|██▎ | ETA: 0:17:19 Progress: 6%|██▎ | ETA: 0:17:17 Progress: 6%|██▎ | ETA: 0:17:15 Progress: 6%|██▍ | ETA: 0:17:12 Progress: 6%|██▍ | ETA: 0:17:10 Progress: 6%|██▍ | ETA: 0:17:15 Progress: 6%|██▌ | ETA: 0:17:15 Progress: 6%|██▌ | ETA: 0:17:12 Progress: 6%|██▌ | ETA: 0:17:10 Progress: 6%|██▋ | ETA: 0:17:08 Progress: 6%|██▋ | ETA: 0:17:04 Progress: 7%|██▋ | ETA: 0:17:09 Progress: 7%|██▊ | ETA: 0:17:06 Progress: 7%|██▊ | ETA: 0:17:05 Progress: 7%|██▊ | ETA: 0:17:03 Progress: 7%|██▉ | ETA: 0:17:01 Progress: 7%|██▉ | ETA: 0:16:59 Progress: 7%|██▉ | ETA: 0:17:04 Progress: 7%|███ | ETA: 0:17:02 Progress: 7%|███ | ETA: 0:16:59 Progress: 7%|███ | ETA: 0:16:58 Progress: 8%|███▏ | ETA: 0:16:56 Progress: 8%|███▏ | ETA: 0:17:00 Progress: 8%|███▏ | ETA: 0:16:59 Progress: 8%|███▎ | ETA: 0:16:57 Progress: 8%|███▎ | ETA: 0:16:55 Progress: 8%|███▎ | ETA: 0:16:53 Progress: 8%|███▍ | ETA: 0:16:51 Progress: 8%|███▍ | ETA: 0:16:53 Progress: 8%|███▍ | ETA: 0:16:52 Progress: 8%|███▌ | ETA: 0:16:49 Progress: 8%|███▌ | ETA: 0:16:46 Progress: 9%|███▌ | ETA: 0:16:44 Progress: 9%|███▋ | ETA: 0:16:42 Progress: 9%|███▋ | ETA: 0:16:46 Progress: 9%|███▋ | ETA: 0:16:44 Progress: 9%|███▊ | ETA: 0:16:42 Progress: 9%|███▊ | ETA: 0:16:40 Progress: 9%|███▊ | ETA: 0:16:38 Progress: 9%|███▉ | ETA: 0:16:40 Progress: 9%|███▉ | ETA: 0:16:39 Progress: 9%|███▉ | ETA: 0:16:37 Progress: 10%|███▉ | ETA: 0:16:35 Progress: 10%|████ | ETA: 0:16:33 Progress: 10%|████ | ETA: 0:16:31 Progress: 10%|████ | ETA: 0:16:34 Progress: 10%|████▏ | ETA: 0:16:32 Progress: 10%|████▏ | ETA: 0:16:30 Progress: 10%|████▏ | ETA: 0:16:28 Progress: 10%|████▎ | ETA: 0:16:26 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:36:28 Progress: 10%|████▏ | ETA: 0:16:40 Progress: 28%|███████████▌ | ETA: 0:04:48 Progress: 49%|████████████████████ | ETA: 0:01:58 Progress: 69%|████████████████████████████▌ | ETA: 0:00:50 Progress: 89%|████████████████████████████████████▋ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 488 records are matched 239.712872 seconds (2.01 G allocations: 106.050 GiB, 13.19% gc time, 0.41% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:16:07 Progress: 0%|▏ | ETA: 0:16:02 Progress: 0%|▏ | ETA: 0:19:03 Progress: 0%|▏ | ETA: 0:18:21 Progress: 1%|▎ | ETA: 0:18:00 Progress: 1%|▎ | ETA: 0:17:52 Progress: 1%|▎ | ETA: 0:17:41 Progress: 1%|▍ | ETA: 0:18:39 Progress: 1%|▍ | ETA: 0:18:30 Progress: 1%|▍ | ETA: 0:18:12 Progress: 1%|▌ | ETA: 0:18:00 Progress: 1%|▌ | ETA: 0:17:50 Progress: 1%|▌ | ETA: 0:18:20 Progress: 1%|▋ | ETA: 0:18:14 Progress: 2%|▋ | ETA: 0:18:00 Progress: 2%|▋ | ETA: 0:17:55 Progress: 2%|▊ | ETA: 0:17:46 Progress: 2%|▊ | ETA: 0:18:06 Progress: 2%|▊ | ETA: 0:18:04 Progress: 2%|▉ | ETA: 0:17:56 Progress: 2%|▉ | ETA: 0:17:50 Progress: 2%|▉ | ETA: 0:17:42 Progress: 2%|█ | ETA: 0:17:34 Progress: 2%|█ | ETA: 0:17:50 Progress: 3%|█ | ETA: 0:17:47 Progress: 3%|█▏ | ETA: 0:17:41 Progress: 3%|█▏ | ETA: 0:17:38 Progress: 3%|█▏ | ETA: 0:17:35 Progress: 3%|█▎ | ETA: 0:17:46 Progress: 3%|█▎ | ETA: 0:17:45 Progress: 3%|█▎ | ETA: 0:17:40 Progress: 3%|█▍ | ETA: 0:17:35 Progress: 3%|█▍ | ETA: 0:17:31 Progress: 3%|█▍ | ETA: 0:17:28 Progress: 4%|█▌ | ETA: 0:17:40 Progress: 4%|█▌ | ETA: 0:17:37 Progress: 4%|█▌ | ETA: 0:17:32 Progress: 4%|█▋ | ETA: 0:17:29 Progress: 4%|█▋ | ETA: 0:17:25 Progress: 4%|█▋ | ETA: 0:17:32 Progress: 4%|█▊ | ETA: 0:17:31 Progress: 4%|█▊ | ETA: 0:17:27 Progress: 4%|█▊ | ETA: 0:17:24 Progress: 4%|█▉ | ETA: 0:17:21 Progress: 5%|█▉ | ETA: 0:17:18 Progress: 5%|█▉ | ETA: 0:17:26 Progress: 5%|██ | ETA: 0:17:24 Progress: 5%|██ | ETA: 0:17:21 Progress: 5%|██ | ETA: 0:17:18 Progress: 5%|██▏ | ETA: 0:17:15 Progress: 5%|██▏ | ETA: 0:17:21 Progress: 5%|██▏ | ETA: 0:17:20 Progress: 5%|██▎ | ETA: 0:17:17 Progress: 5%|██▎ | ETA: 0:17:15 Progress: 6%|██▎ | ETA: 0:17:12 Progress: 6%|██▍ | ETA: 0:17:09 Progress: 6%|██▍ | ETA: 0:17:15 Progress: 6%|██▍ | ETA: 0:17:14 Progress: 6%|██▍ | ETA: 0:17:11 Progress: 6%|██▌ | ETA: 0:17:09 Progress: 6%|██▌ | ETA: 0:17:07 Progress: 6%|██▌ | ETA: 0:17:12 Progress: 6%|██▋ | ETA: 0:17:12 Progress: 6%|██▋ | ETA: 0:17:09 Progress: 7%|██▋ | ETA: 0:17:06 Progress: 7%|██▊ | ETA: 0:17:04 Progress: 7%|██▊ | ETA: 0:17:02 Progress: 7%|██▊ | ETA: 0:17:07 Progress: 7%|██▉ | ETA: 0:17:05 Progress: 7%|██▉ | ETA: 0:17:03 Progress: 7%|██▉ | ETA: 0:17:00 Progress: 7%|███ | ETA: 0:16:58 Progress: 7%|███ | ETA: 0:17:03 Progress: 7%|███ | ETA: 0:17:02 Progress: 8%|███▏ | ETA: 0:16:59 Progress: 8%|███▏ | ETA: 0:16:57 Progress: 8%|███▏ | ETA: 0:16:55 Progress: 8%|███▎ | ETA: 0:16:53 Progress: 8%|███▎ | ETA: 0:16:57 Progress: 8%|███▎ | ETA: 0:16:55 Progress: 8%|███▍ | ETA: 0:16:53 Progress: 8%|███▍ | ETA: 0:16:50 Progress: 8%|███▍ | ETA: 0:16:48 Progress: 8%|███▌ | ETA: 0:16:46 Progress: 9%|███▌ | ETA: 0:16:49 Progress: 9%|███▌ | ETA: 0:16:47 Progress: 9%|███▋ | ETA: 0:16:45 Progress: 9%|███▋ | ETA: 0:16:42 Progress: 9%|███▋ | ETA: 0:16:40 Progress: 9%|███▊ | ETA: 0:16:43 Progress: 9%|███▊ | ETA: 0:16:41 Progress: 9%|███▊ | ETA: 0:16:39 Progress: 9%|███▉ | ETA: 0:16:37 Progress: 9%|███▉ | ETA: 0:16:35 Progress: 10%|███▉ | ETA: 0:16:38 Progress: 10%|████ | ETA: 0:16:37 Progress: 10%|████ | ETA: 0:16:35 Progress: 10%|████ | ETA: 0:16:32 Progress: 10%|████▏ | ETA: 0:16:30 Progress: 10%|████▏ | ETA: 0:16:29 Progress: 10%|████▏ | ETA: 0:16:31 Progress: 10%|████▏ | ETA: 0:16:29 Progress: 10%|████▎ | ETA: 0:16:27 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:15:42 Progress: 22%|█████████▏ | ETA: 0:06:20 Progress: 44%|██████████████████▏ | ETA: 0:02:20 Progress: 64%|██████████████████████████▎ | ETA: 0:01:03 Progress: 88%|████████████████████████████████████▏ | ETA: 0:00:15 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 0 records are matched 236.586495 seconds (2.01 G allocations: 106.050 GiB, 12.96% gc time, 0.38% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m01.8s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:29:07 Progress: 19%|███████▋ | ETA: 0:07:35 Progress: 35%|██████████████▌ | ETA: 0:03:13 Progress: 56%|███████████████████████▏ | ETA: 0:01:23 Progress: 79%|████████████████████████████████▎ | ETA: 0:00:30 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 833 records are matched 119.515419 seconds (1.01 G allocations: 53.815 GiB, 11.89% gc time, 0.51% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:56:20 Progress: 21%|████████▋ | ETA: 0:06:44 Progress: 44%|██████████████████ | ETA: 0:02:17 Progress: 67%|███████████████████████████▌ | ETA: 0:00:54 Progress: 89%|████████████████████████████████████▌ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: 493 records are matched 121.066562 seconds (1.01 G allocations: 53.814 GiB, 11.39% gc time, 0.52% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:50:12 Progress: 21%|████████▋ | ETA: 0:06:42 Progress: 42%|█████████████████▏ | ETA: 0:02:31 Progress: 61%|█████████████████████████ | ETA: 0:01:10 Progress: 85%|███████████████████████████████████ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 0 records are matched 120.583180 seconds (1.01 G allocations: 53.814 GiB, 11.45% gc time, 0.52% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m03.3s 1.197464 seconds (1.15 M allocations: 65.823 MiB, 1.63% gc time, 82.13% compilation time) 1.034220 seconds (1.06 M allocations: 62.766 MiB, 79.97% compilation time) 1.031379 seconds (1.06 M allocations: 61.811 MiB, 2.50% gc time, 79.91% compilation time) 0.420185 seconds (176.12 k allocations: 10.171 MiB, 99.96% compilation time) 0.011420 seconds (6.07 k allocations: 392.633 KiB, 96.93% compilation time) 0.010234 seconds (2.62 k allocations: 165.727 KiB, 95.19% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 10.0s 0.969710 seconds (958.44 k allocations: 56.416 MiB, 81.56% compilation time) 1.378658 seconds (817.22 k allocations: 50.545 MiB, 33.39% gc time, 53.73% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 7.3s Test Summary: | Pass Total Time convert_ds | 5 5 1.3s 0.121151 seconds (525.04 k allocations: 30.675 MiB, 27.02% compilation time) 0.702809 seconds (625.50 k allocations: 36.985 MiB, 86.74% 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 0.066274 seconds (520.58 k allocations: 32.160 MiB) 0.629457 seconds (583.55 k allocations: 36.184 MiB, 2.82% gc time, 85.90% 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 convert to transpose functions: Test Failed at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 Expression: all(out[1358:var"end", :] .== 0.0) Evaluated: all(Bool[0 0 … 0 0; 0 0 … 0 0; … ; 0 0 … 0 0; 0 0 … 0 0]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] [2] macro expansion @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.191588 seconds (1.56 M allocations: 62.080 MiB, 40.44% gc time, 5.38% compilation time) 0.691508 seconds (1.68 M allocations: 69.846 MiB, 84.16% 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 Fail Total Time convert to transpose functions | 12 1 13 13.0s RNG of the outermost testset: Xoshiro(0xa7d0d170cebaa6c3, 0x2423c52142d5a5da, 0xaf65e5723f774693, 0x4268ac9686fbbafa, 0x5216542d85721606) ERROR: LoadError: Some tests did not pass: 12 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:72 in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/runtests.jl:17 Testing failed after 1193.66s ERROR: LoadError: Package VCFTools errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1648.93s: package has test failures