Package evaluation to test VCFTools on Julia 1.14.0-DEV.1699 (9484a92029*) started at 2026-02-10T21:20:19.945 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.13s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed MacroTools ────────────── v0.5.16 Installed DelimitedFiles ────────── v1.9.1 Installed DataStructures ────────── v0.19.3 Installed FillArrays ────────────── v1.16.0 Installed CommonSolve ───────────── v0.2.6 Installed HypergeometricFunctions ─ v0.3.28 Installed ConstructionBase ──────── v1.6.0 Installed CodecZlib ─────────────── v0.7.8 Installed OrderedCollections ────── v1.8.1 Installed AliasTables ───────────── v1.1.3 Installed StatsBase ─────────────── v0.34.10 Installed TranscodingStreams ────── v0.11.3 Installed SIMD ──────────────────── v3.7.2 Installed DataAPI ───────────────── v1.16.0 Installed StatsAPI ──────────────── v1.8.0 Installed Combinatorics ─────────── v1.1.0 Installed Statistics ────────────── v1.11.1 Installed HypothesisTests ───────── v0.11.6 Installed PrecompileTools ───────── v1.3.3 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed ProgressMeter ─────────── v1.11.0 Installed IrrationalConstants ───── v0.2.6 Installed QuadGK ────────────────── v2.11.2 Installed LogExpFunctions ───────── v0.3.29 Installed Roots ─────────────────── v2.2.10 Installed Distributions ─────────── v0.25.123 Installed Rmath ─────────────────── v0.9.0 Installed BufferedStreams ───────── v1.2.2 Installed PtrArrays ─────────────── v1.3.0 Installed StatsFuns ─────────────── v1.5.2 Installed InverseFunctions ──────── v0.1.17 Installed SpecialFunctions ──────── v2.6.1 Installed BioGenerics ───────────── v0.1.5 Installed VCFTools ──────────────── v0.2.10 Installed Reexport ──────────────── v1.2.2 Installed Preferences ───────────── v1.5.1 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed PDMats ────────────────── v0.11.37 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.43 Installed Automa ────────────────── v1.1.0 Installed BGZFStreams ───────────── v0.3.2 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 v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [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 v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 8.52s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4624.6 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4670.8 ms ✓ MacroTools 1726.8 ms ✓ InlineStrings 867.7 ms ✓ Reexport 1205.0 ms ✓ Statistics 966.0 ms ✓ DataAPI 1229.9 ms ✓ ConstructionBase 2302.0 ms ✓ IrrationalConstants 895.3 ms ✓ DataValueInterfaces 999.0 ms ✓ StatsAPI 1374.5 ms ✓ OrderedCollections 981.9 ms ✓ InvertedIndices 1059.3 ms ✓ InverseFunctions 975.3 ms ✓ CompositionsBase 1250.6 ms ✓ DocStringExtensions 2244.7 ms ✓ Combinatorics 1069.4 ms ✓ WorkerUtilities 2273.5 ms ✓ FillArrays 1134.2 ms ✓ BufferedStreams 921.8 ms ✓ PtrArrays 853.7 ms ✓ CommonSolve 1368.1 ms ✓ TranscodingStreams 843.9 ms ✓ IteratorInterfaceExtensions 923.7 ms ✓ LaTeXStrings 1953.7 ms ✓ Crayons 1919.6 ms ✓ PDMats 1065.3 ms ✓ DelimitedFiles 1894.0 ms ✓ ProgressMeter 2302.7 ms ✓ SentinelArrays 1258.2 ms ✓ Compat 1231.5 ms ✓ Preferences 1444.3 ms ✓ Statistics → SparseArraysExt 1049.5 ms ✓ Missings 1083.5 ms ✓ PooledArrays 863.8 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3731.5 ms ✓ DataStructures 1765.1 ms ✓ InverseFunctions → InverseFunctionsTestExt 956.6 ms ✓ InverseFunctions → InverseFunctionsDatesExt 873.4 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1491.3 ms ✓ LogExpFunctions 1601.3 ms ✓ FillArrays → FillArraysSparseArraysExt 1071.2 ms ✓ FillArrays → FillArraysStatisticsExt 1055.3 ms ✓ AliasTables 1036.4 ms ✓ BioGenerics 1077.0 ms ✓ CodecZlib 873.9 ms ✓ TableTraits 1560.7 ms ✓ FillArrays → FillArraysPDMatsExt 942.1 ms ✓ Compat → CompatLinearAlgebraExt 1298.5 ms ✓ JLLWrappers 1028.6 ms ✓ PrecompileTools 1225.9 ms ✓ SortingAlgorithms 2526.6 ms ✓ QuadGK 5572.0 ms ✓ Accessors 895.2 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1099.3 ms ✓ BGZFStreams 1902.2 ms ✓ Tables 2204.7 ms ✓ FilePathsBase 1530.4 ms ✓ Rmath_jll 1548.7 ms ✓ OpenSpecFun_jll 3472.2 ms ✓ StringManipulation 15321.1 ms ✓ SIMD 17884.2 ms ✓ Parsers 4832.7 ms ✓ StatsBase 2412.3 ms ✓ Accessors → LinearAlgebraExt 1821.4 ms ✓ Accessors → TestExt 2979.9 ms ✓ FilePathsBase → FilePathsBaseTestExt 1025.7 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1601.6 ms ✓ Rmath 5253.2 ms ✓ SpecialFunctions 39676.6 ms ✓ PrettyTables 18106.1 ms ✓ Automa 1046.9 ms ✓ InlineStrings → ParsersExt 1547.4 ms ✓ PDMats → StatsBaseExt 7293.7 ms ✓ Roots 2366.8 ms ✓ HypergeometricFunctions 83578.8 ms ✓ DataFrames [ Info: Compiling VCF parser... 15879.1 ms ✓ VariantCallFormat 2641.4 ms ✓ WeakRefStrings 3096.2 ms ✓ StatsFuns 26950.5 ms ✓ CSV 1086.4 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9236.5 ms ✓ Distributions 3589.0 ms ✓ Distributions → DistributionsTestExt 4516.7 ms ✓ HypothesisTests 4977.5 ms ✓ VCFTools 84 dependencies successfully precompiled in 369 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 395.69s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_28X4fs/Project.toml` [336ed68f] CSV v0.10.15 [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 v2.6.1 [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_28X4fs/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 v0.10.15 [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 v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [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 v1.3.1+2 [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 3.1s Test Summary: | Pass Total Time openvcf | 4 4 2.4s 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 4.0s ┌ 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: 0:29:51 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 13.198527 seconds (8.99 M allocations: 544.543 MiB, 1.25% gc time, 95.79% compilation time: 15% of which was recompilation) 0.405957 seconds (2.37 M allocations: 141.167 MiB, 10.58% gc time, 15.24% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:30:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.602377 seconds (3.90 M allocations: 236.557 MiB, 14.29% gc time, 74.57% compilation time: <1% of which was recompilation) 0.417607 seconds (2.37 M allocations: 141.173 MiB, 3.23% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 20.9s 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 1.7s 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 1.6s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:05 Progress: 0%|▏ | ETA: 0:17:17 Progress: 0%|▏ | ETA: 0:20:05 Progress: 0%|▏ | ETA: 0:19:22 Progress: 0%|▎ | ETA: 0:18:48 Progress: 1%|▎ | ETA: 0:18:20 Progress: 1%|▎ | ETA: 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Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:30:32 Progress: 16%|██████▌ | ETA: 0:09:47 Progress: 37%|███████████████▍ | ETA: 0:03:05 Progress: 59%|████████████████████████▏ | ETA: 0:01:18 Progress: 77%|███████████████████████████████▌ | ETA: 0:00:34 Progress: 98%|████████████████████████████████████████▎| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: 823 records are matched 238.802814 seconds (2.01 G allocations: 106.138 GiB, 13.69% gc time, 0.53% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:05 Progress: 0%|▏ | ETA: 0:16:53 Progress: 0%|▏ | ETA: 0:16:52 Progress: 0%|▏ | ETA: 0:17:00 Progress: 0%|▎ | ETA: 0:18:34 Progress: 1%|▎ | ETA: 0:18:14 Progress: 1%|▎ | ETA: 0:18:00 Progress: 1%|▍ | ETA: 0:17:48 Progress: 1%|▍ | ETA: 0:17:37 Progress: 1%|▍ | ETA: 0:18:28 Progress: 1%|▌ | ETA: 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Progress: 8%|███▌ | ETA: 0:16:53 Progress: 9%|███▌ | ETA: 0:16:51 Progress: 9%|███▌ | ETA: 0:16:54 Progress: 9%|███▋ | ETA: 0:16:53 Progress: 9%|███▋ | ETA: 0:16:51 Progress: 9%|███▋ | ETA: 0:16:49 Progress: 9%|███▊ | ETA: 0:16:46 Progress: 9%|███▊ | ETA: 0:16:44 Progress: 9%|███▊ | ETA: 0:16:47 Progress: 9%|███▉ | ETA: 0:16:45 Progress: 9%|███▉ | ETA: 0:16:42 Progress: 10%|███▉ | ETA: 0:16:40 Progress: 10%|████ | ETA: 0:16:38 Progress: 10%|████ | ETA: 0:16:41 Progress: 10%|████ | ETA: 0:16:39 Progress: 10%|████▏ | ETA: 0:16:38 Progress: 10%|████▏ | ETA: 0:16:35 Progress: 10%|████▏ | ETA: 0:16:33 Progress: 10%|████▎ | ETA: 0:16:35 Progress: 10%|████▎ | ETA: 0:16:34 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:37:34 Progress: 17%|███████ | ETA: 0:08:53 Progress: 38%|███████████████▋ | ETA: 0:03:01 Progress: 61%|█████████████████████████ | ETA: 0:01:12 Progress: 83%|██████████████████████████████████ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 0 records are matched 239.541513 seconds (2.01 G allocations: 106.120 GiB, 13.78% gc time, 0.32% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m48.0s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:11:46 Progress: 19%|████████ | ETA: 0:07:31 Progress: 38%|███████████████▊ | ETA: 0:02:55 Progress: 56%|███████████████████████▏ | ETA: 0:01:26 Progress: 77%|███████████████████████████████▌ | ETA: 0:00:34 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 833 records are matched 123.244549 seconds (1.02 G allocations: 53.885 GiB, 11.73% gc time, 0.43% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:37:32 Progress: 20%|████████▏ | ETA: 0:07:08 Progress: 42%|█████████████████▏ | ETA: 0:02:28 Progress: 64%|██████████████████████████▏ | ETA: 0:01:01 Progress: 84%|██████████████████████████████████▎ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 493 records are matched 119.891327 seconds (1.02 G allocations: 53.884 GiB, 11.53% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:08:37 Progress: 20%|████████▍ | ETA: 0:07:03 Progress: 40%|████████████████▋ | ETA: 0:02:42 Progress: 60%|████████████████████████▊ | ETA: 0:01:13 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 0 records are matched 123.234744 seconds (1.02 G allocations: 53.884 GiB, 12.20% gc time, 0.46% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m09.0s 1.077695 seconds (1.14 M allocations: 65.517 MiB, 84.05% compilation time) 0.966107 seconds (1.05 M allocations: 62.387 MiB, 79.56% compilation time) 0.998907 seconds (1.05 M allocations: 61.411 MiB, 4.14% gc time, 82.85% compilation time) 0.431705 seconds (175.78 k allocations: 10.153 MiB, 99.96% compilation time) 0.011838 seconds (6.06 k allocations: 389.992 KiB, 96.02% compilation time) 0.009896 seconds (2.62 k allocations: 165.320 KiB, 95.54% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.5s 0.987185 seconds (953.00 k allocations: 56.245 MiB, 77.38% compilation time) 0.919933 seconds (814.28 k allocations: 50.513 MiB, 9.93% gc time, 81.50% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.4s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.099991 seconds (525.08 k allocations: 30.676 MiB, 30.90% compilation time) 0.596560 seconds (624.71 k allocations: 36.979 MiB, 87.62% 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 0.086086 seconds (520.58 k allocations: 32.160 MiB, 20.90% gc time) 0.509978 seconds (583.30 k allocations: 36.213 MiB, 86.95% 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:782 [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:2244 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.130343 seconds (1.56 M allocations: 62.080 MiB, 6.94% compilation time) 0.639950 seconds (1.68 M allocations: 69.790 MiB, 8.74% gc time, 73.39% 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 12.5s RNG of the outermost testset: Xoshiro(0x238c04a3c725147a, 0x6b750a829b520405, 0xac9f90c8c3939131, 0xd825aba2bafcfcdf, 0xae10a98a87e7e097) 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 1177.95s 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:3122 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2987 [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:572 [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:548 [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:309 [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 1636.86s: package has test failures