Package evaluation to test VCFTools on Julia 1.12.4 (0f21d93eaa*) started at 2026-01-27T01:03:15.545 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 9.34s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed StatsFuns ─────────────── v1.5.2 Installed IrrationalConstants ───── v0.2.6 Installed Rmath ─────────────────── v0.9.0 Installed SIMD ──────────────────── v3.7.2 Installed HypergeometricFunctions ─ v0.3.28 Installed BioGenerics ───────────── v0.1.5 Installed Accessors ─────────────── v0.1.43 Installed Preferences ───────────── v1.5.1 Installed PtrArrays ─────────────── v1.3.0 Installed DataAPI ───────────────── v1.16.0 Installed JLLWrappers ───────────── v1.7.1 Installed PDMats ────────────────── v0.11.37 Installed ProgressMeter ─────────── v1.11.0 Installed SpecialFunctions ──────── v2.6.1 Installed Roots ─────────────────── v2.2.10 Installed PrecompileTools ───────── v1.3.3 Installed ConstructionBase ──────── v1.6.0 Installed OrderedCollections ────── v1.8.1 Installed Combinatorics ─────────── v1.1.0 Installed DelimitedFiles ────────── v1.9.1 Installed TranscodingStreams ────── v0.11.3 Installed BGZFStreams ───────────── v0.3.2 Installed Rmath_jll ─────────────── v0.5.1+0 Installed Reexport ──────────────── v1.2.2 Installed FillArrays ────────────── v1.16.0 Installed VCFTools ──────────────── v0.2.10 Installed QuadGK ────────────────── v2.11.2 Installed HypothesisTests ───────── v0.11.6 Installed VariantCallFormat ─────── v0.5.9 Installed LogExpFunctions ───────── v0.3.29 Installed Statistics ────────────── v1.11.1 Installed DataStructures ────────── v0.19.3 Installed AliasTables ───────────── v1.1.3 Installed BufferedStreams ───────── v1.2.2 Installed StatsAPI ──────────────── v1.8.0 Installed MacroTools ────────────── v0.5.16 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Distributions ─────────── v0.25.123 Installed CompositionsBase ──────── v0.1.2 Installed InverseFunctions ──────── v0.1.17 Installed CodecZlib ─────────────── v0.7.8 Installed CommonSolve ───────────── v0.2.6 Installed Missings ──────────────── v1.2.0 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed Automa ────────────────── v1.1.0 Installed StatsBase ─────────────── v0.34.10 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.12/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.12/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 v1.12.0 [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 [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 v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 9.57s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4434.9 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompiling packages... 2284.3 ms ✓ Combinatorics 4338.0 ms ✓ OrderedCollections 857.0 ms ✓ DataValueInterfaces 1975.1 ms ✓ FillArrays 880.5 ms ✓ LaTeXStrings 896.3 ms ✓ InvertedIndices 959.7 ms ✓ InverseFunctions 792.7 ms ✓ Reexport 1131.2 ms ✓ DocStringExtensions 1839.4 ms ✓ InlineStrings 1034.5 ms ✓ BufferedStreams 1136.8 ms ✓ Statistics 5057.6 ms ✓ IrrationalConstants 793.3 ms ✓ CommonSolve 4175.5 ms ✓ ConstructionBase 776.5 ms ✓ IteratorInterfaceExtensions 884.9 ms ✓ DataAPI 1096.8 ms ✓ WorkerUtilities 903.9 ms ✓ StatsAPI 5022.6 ms ✓ Crayons 827.6 ms ✓ CompositionsBase 1927.3 ms ✓ ProgressMeter 7255.1 ms ✓ MacroTools 823.2 ms ✓ PtrArrays 1307.3 ms ✓ TranscodingStreams 1014.4 ms ✓ DelimitedFiles 2249.6 ms ✓ SentinelArrays 4227.4 ms ✓ Compat 1147.6 ms ✓ Preferences 1846.8 ms ✓ PDMats 3673.0 ms ✓ DataStructures 1460.6 ms ✓ FillArrays → FillArraysSparseArraysExt 930.7 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1829.9 ms ✓ InverseFunctions → InverseFunctionsTestExt 1317.2 ms ✓ Statistics → SparseArraysExt 905.1 ms ✓ FillArrays → FillArraysStatisticsExt 1465.5 ms ✓ LogExpFunctions 857.1 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 766.2 ms ✓ TableTraits 1045.7 ms ✓ PooledArrays 3897.0 ms ✓ Missings 856.2 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 998.0 ms ✓ AliasTables 974.9 ms ✓ CodecZlib 3902.9 ms ✓ BioGenerics 900.4 ms ✓ Compat → CompatLinearAlgebraExt 885.1 ms ✓ PrecompileTools 1216.6 ms ✓ JLLWrappers 1339.3 ms ✓ FillArrays → FillArraysPDMatsExt 1137.3 ms ✓ SortingAlgorithms 5135.5 ms ✓ QuadGK 835.3 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 4825.7 ms ✓ Tables 7457.3 ms ✓ Accessors 898.6 ms ✓ BGZFStreams 1978.1 ms ✓ FilePathsBase 3272.6 ms ✓ StringManipulation 18175.6 ms ✓ SIMD 18230.8 ms ✓ Parsers 1243.6 ms ✓ Rmath_jll 1197.8 ms ✓ OpenSpecFun_jll 6062.1 ms ✓ StatsBase 1833.1 ms ✓ Accessors → LinearAlgebraExt 1618.3 ms ✓ Accessors → TestExt 2821.9 ms ✓ FilePathsBase → FilePathsBaseTestExt 1320.4 ms ✓ FilePathsBase → FilePathsBaseMmapExt 37870.8 ms ✓ PrettyTables 21064.9 ms ✓ Automa 830.8 ms ✓ InlineStrings → ParsersExt 1327.8 ms ✓ Rmath 4708.3 ms ✓ SpecialFunctions 1203.8 ms ✓ PDMats → StatsBaseExt 8026.7 ms ✓ Roots 85160.7 ms ✓ DataFrames 20552.1 ms ✓ VariantCallFormat 2372.4 ms ✓ WeakRefStrings 2261.8 ms ✓ HypergeometricFunctions 33491.4 ms ✓ CSV 6211.5 ms ✓ StatsFuns 984.0 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9679.2 ms ✓ Distributions 3383.5 ms ✓ Distributions → DistributionsTestExt 4303.8 ms ✓ HypothesisTests 6796.6 ms ✓ VCFTools 84 dependencies successfully precompiled in 417 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 441.14s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_DF1OQb/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 v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_DF1OQb/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 v1.12.0 [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 [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 v1.12.0 [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 v8.15.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 4.0s Test Summary: | Pass Total Time openvcf | 4 4 2.7s 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 3.7s ┌ 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: 0:42:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 16.233845 seconds (11.42 M allocations: 636.489 MiB, 4.36% gc time, 96.06% compilation time: 22% of which was recompilation) 0.428406 seconds (2.40 M allocations: 143.898 MiB, 5.91% gc time, 21.23% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:34:50 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.615256 seconds (4.36 M allocations: 255.915 MiB, 2.49% gc time, 86.61% compilation time) 0.454879 seconds (2.38 M allocations: 143.351 MiB, 5.66% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 24.5s 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 2.1s 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: 0:17:30 Progress: 0%|▏ | ETA: 0:21:56 Progress: 0%|▏ | ETA: 0:20:06 Progress: 0%|▏ | ETA: 0:19:06 Progress: 0%|▎ | ETA: 0:18:32 Progress: 1%|▎ | ETA: 0:19:39 Progress: 1%|▎ | ETA: 0:19:11 Progress: 1%|▍ | ETA: 0:18:47 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100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:57:53 Progress: 21%|████████▍ | ETA: 0:06:35 Progress: 40%|████████████████▎ | ETA: 0:02:37 Progress: 67%|███████████████████████████▌ | ETA: 0:00:51 Progress: 94%|██████████████████████████████████████▍ | ETA: 0:00:07 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 823 records are matched 236.455393 seconds (2.01 G allocations: 106.139 GiB, 12.14% gc time, 0.61% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:13 Progress: 0%|▏ | ETA: 0:17:01 Progress: 0%|▏ | ETA: 0:20:17 Progress: 0%|▏ | ETA: 0:19:25 Progress: 0%|▎ | ETA: 0:18:55 Progress: 1%|▎ | ETA: 0:18:37 Progress: 1%|▎ | ETA: 0:18:08 Progress: 1%|▍ | ETA: 0:18:44 Progress: 1%|▍ | ETA: 0:18:39 Progress: 1%|▍ | ETA: 0:18:26 Progress: 1%|▌ | ETA: 0:18:16 Progress: 1%|▌ | ETA: 0:18:06 Progress: 1%|▌ | ETA: 0:17:59 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10%|████▎ | ETA: 0:17:41 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 22:04:14 Progress: 20%|████████▏ | ETA: 0:07:58 Progress: 39%|████████████████▏ | ETA: 0:03:04 Progress: 58%|███████████████████████▉ | ETA: 0:01:27 Progress: 77%|███████████████████████████████▊ | ETA: 0:00:36 Progress: 99%|████████████████████████████████████████▋| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: 0 records are matched 264.210947 seconds (2.01 G allocations: 106.122 GiB, 12.47% gc time, 0.36% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m38.6s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:38:47 Progress: 18%|███████▌ | ETA: 0:08:39 Progress: 36%|██████████████▉ | ETA: 0:03:26 Progress: 56%|███████████████████████▏ | ETA: 0:01:32 Progress: 76%|███████████████████████████████▎ | ETA: 0:00:37 Progress: 96%|███████████████████████████████████████▌ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 833 records are matched 140.333182 seconds (1.02 G allocations: 53.886 GiB, 11.88% gc time, 0.42% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:33:14 Progress: 30%|████████████▍ | ETA: 0:03:52 Progress: 56%|███████████████████████ | ETA: 0:01:19 Progress: 89%|████████████████████████████████████▍ | ETA: 0:00:13 Progress: 100%|█████████████████████████████████████████| Time: 0:01:42 [ Info: 493 records are matched 120.833907 seconds (1.02 G allocations: 53.886 GiB, 11.23% gc time, 0.52% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:02:01 Progress: 9%|███▊ | ETA: 0:18:31 Progress: 27%|███████████▏ | ETA: 0:05:05 Progress: 48%|███████████████████▋ | ETA: 0:02:05 Progress: 70%|████████████████████████████▊ | ETA: 0:00:50 Progress: 92%|█████████████████████████████████████▋ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:01:57 [ Info: 0 records are matched 136.376791 seconds (1.02 G allocations: 53.885 GiB, 11.48% gc time, 0.41% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m40.0s 1.158347 seconds (1.42 M allocations: 74.817 MiB, 83.05% compilation time) 1.139422 seconds (1.30 M allocations: 70.625 MiB, 2.16% gc time, 79.31% compilation time) 1.088084 seconds (1.30 M allocations: 69.648 MiB, 82.03% compilation time) 0.485684 seconds (238.04 k allocations: 12.346 MiB, 99.97% compilation time) 0.010586 seconds (7.05 k allocations: 427.023 KiB, 96.26% compilation time) 0.009314 seconds (2.73 k allocations: 170.367 KiB, 96.38% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.3s 0.888284 seconds (1.05 M allocations: 58.349 MiB, 3.49% gc time, 78.69% compilation time) 0.771636 seconds (938.48 k allocations: 54.349 MiB, 3.57% gc time, 71.76% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.4s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.124314 seconds (526.31 k allocations: 30.727 MiB, 25.64% compilation time) 0.724104 seconds (672.53 k allocations: 38.430 MiB, 3.01% gc time, 83.93% 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 0.084963 seconds (520.58 k allocations: 32.160 MiB) 0.375900 seconds (606.97 k allocations: 36.941 MiB, 4.26% gc time, 73.41% 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:end, :] .== 0.0) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:680 [inlined] [2] macro expansion @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.131044 seconds (1.56 M allocations: 62.084 MiB, 6.48% compilation time) 0.751710 seconds (1.74 M allocations: 71.961 MiB, 76.65% 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 10.8s RNG of the outermost testset: Xoshiro(0x7bb22ad49749fdef, 0xb99a042bfdf566b6, 0x4ac2c4ba8fabc32b, 0x0e8928e22159a18e, 0x840e2d2c48f86cca) 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 1266.13s ERROR: LoadError: Package VCFTools errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2535 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2384 [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/v1.12/Pkg/src/API.jl:538 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1749.37s: package has test failures