Package evaluation to test VCFTools on Julia 1.14.0-DEV.3071 (c76331c927*) started at 2026-08-30T20:31:30.582 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 17.13s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.2+0 Installed CommonSolve ───────────── v0.2.14 Installed FillArrays ────────────── v1.17.0 Installed DataStructures ────────── v0.19.6 Installed MacroTools ────────────── v0.5.16 Installed DelimitedFiles ────────── v1.9.1 Installed CompositionsBase ──────── v0.1.2 Installed VCFTools ──────────────── v0.2.10 Installed HypergeometricFunctions ─ v0.3.30 Installed CodecZlib ─────────────── v0.7.9 Installed StatsBase ─────────────── v0.34.13 Installed OrderedCollections ────── v2.0.1 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed TranscodingStreams ────── v0.11.3 Installed Statistics ────────────── v1.11.4 Installed Combinatorics ─────────── v1.1.0 Installed HypothesisTests ───────── v0.11.8 Installed DataAPI ───────────────── v1.16.0 Installed ProgressMeter ─────────── v1.11.0 Installed PrecompileTools ───────── v1.3.4 Installed IrrationalConstants ───── v0.2.6 Installed LogExpFunctions ───────── v1.0.1 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed StatsAPI ──────────────── v1.8.0 Installed Roots ─────────────────── v3.0.7 Installed BufferedStreams ───────── v1.2.2 Installed QuadGK ────────────────── v2.11.3 Installed Distributions ─────────── v0.25.131 Installed Gamma ─────────────────── v1.2.0 Installed StatsFuns ─────────────── v2.2.1 Installed SpecialFunctions ──────── v2.9.0 Installed Rmath ─────────────────── v0.9.0 Installed BioGenerics ───────────── v0.1.5 Installed PtrArrays ─────────────── v1.4.0 Installed Reexport ──────────────── v1.2.2 Installed InverseFunctions ──────── v0.1.17 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.8.0 Installed Preferences ───────────── v1.5.2 Installed Automa ────────────────── v1.2.0 Installed SortingAlgorithms ─────── v1.2.3 Installed PDMats ────────────────── v0.11.41 Installed Accessors ─────────────── v0.1.45 Installed VariantCallFormat ─────── v0.5.9 Installed BGZFStreams ───────────── v0.3.2 Installed DocStringExtensions ───── v0.9.5 Installing 2 artifacts Installed artifact Rmath 111.3 KiB Installed artifact OpenSpecFun 105.4 KiB Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.2.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.9 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.14 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.6 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.131 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.17.0 [a0844989] + Gamma v1.2.0 [34004b35] + HypergeometricFunctions v0.3.30 [09f84164] + HypothesisTests v0.11.8 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.8.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v2.0.1 [90014a1f] + PDMats v0.11.41 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.7 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.9.0 [10745b16] + Statistics v1.11.4 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.13 [4c63d2b9] + StatsFuns v2.2.1 [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 v0.5.2+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [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 v1.5.7+0 [4536629a] + OpenBLAS_jll v0.3.34+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 8.9s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4.7 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 3.5 s ✓ MacroTools 1.4 s ✓ InlineStrings 0.6 s ✓ Reexport 0.9 s ✓ Statistics 0.6 s ✓ DataAPI 0.8 s ✓ ConstructionBase 2.4 s ✓ IrrationalConstants 0.7 s ✓ DataValueInterfaces 0.7 s ✓ StatsAPI 1.1 s ✓ OrderedCollections 0.6 s ✓ InvertedIndices 0.6 s ✓ InverseFunctions 0.6 s ✓ CompositionsBase 0.9 s ✓ DocStringExtensions 1.9 s ✓ Combinatorics 0.7 s ✓ WorkerUtilities 2.3 s ✓ FillArrays 0.8 s ✓ BufferedStreams 0.7 s ✓ PtrArrays 1.0 s ✓ TranscodingStreams 0.5 s ✓ IteratorInterfaceExtensions 0.6 s ✓ LaTeXStrings 2.4 s ✓ Crayons 2.2 s ✓ PDMats 0.7 s ✓ DelimitedFiles 2.5 s ✓ ProgressMeter 2.5 s ✓ SentinelArrays 1.1 s ✓ Compat 1.3 s ✓ Preferences 1.9 s ✓ Statistics → SparseArraysExt 0.7 s ✓ Missings 0.8 s ✓ PooledArrays 0.5 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3.6 s ✓ DataStructures 1.7 s ✓ InverseFunctions → InverseFunctionsTestExt 1.3 s ✓ InverseFunctions → InverseFunctionsDatesExt 0.6 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.3 s ✓ LogExpFunctions 1.9 s ✓ FillArrays → FillArraysSparseArraysExt 0.9 s ✓ FillArrays → FillArraysStatisticsExt 0.7 s ✓ AliasTables 0.7 s ✓ BioGenerics 0.7 s ✓ CodecZlib 0.5 s ✓ TableTraits 1.9 s ✓ FillArrays → FillArraysPDMatsExt 0.7 s ✓ Compat → CompatLinearAlgebraExt 1.8 s ✓ JLLWrappers 1.1 s ✓ PrecompileTools 0.8 s ✓ SortingAlgorithms 1.8 s ✓ QuadGK 4.2 s ✓ Accessors 0.6 s ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1.5 s ✓ Gamma 0.7 s ✓ BGZFStreams 1.7 s ✓ Tables 1.9 s ✓ FilePathsBase 1.7 s ✓ Rmath_jll 1.1 s ✓ OpenSpecFun_jll 17.4 s ✓ Automa 6.2 s ✓ StringManipulation 1.6 s ✓ CommonSolve 11.1 s ✓ Parsers 4.7 s ✓ StatsBase 2.3 s ✓ Accessors → LinearAlgebraExt 1.9 s ✓ Accessors → TestExt 2.0 s ✓ HypergeometricFunctions 2.9 s ✓ FilePathsBase → FilePathsBaseTestExt 0.9 s ✓ FilePathsBase → FilePathsBaseMmapExt 1.5 s ✓ Rmath 5.2 s ✓ SpecialFunctions [ Info: Compiling VCF parser... 14.4 s ✓ VariantCallFormat 42.4 s ✓ PrettyTables 0.8 s ✓ InlineStrings → ParsersExt 1.8 s ✓ PDMats → StatsBaseExt 5.3 s ✓ Roots 2.6 s ✓ StatsFuns 85.1 s ✓ DataFrames 2.6 s ✓ WeakRefStrings 1.0 s ✓ StatsFuns → StatsFunsInverseFunctionsExt 28.7 s ✓ CSV 11.1 s ✓ Distributions 4.6 s ✓ Distributions → DistributionsTestExt 4.9 s ✓ HypothesisTests 5.6 s ✓ VCFTools 84 dependencies successfully precompiled in 345 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 367.55s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_WuVymw/Project.toml` [336ed68f] CSV v0.10.17 [944b1d66] CodecZlib v0.7.9 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.131 [09f84164] HypothesisTests v0.11.8 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.9.0 [2913bbd2] StatsBase v0.34.13 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_WuVymw/Manifest.toml` [7d9f7c33] Accessors v0.1.45 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.2.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.17 [944b1d66] CodecZlib v0.7.9 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.14 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.2.0 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.131 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.17.0 [a0844989] Gamma v1.2.0 [34004b35] HypergeometricFunctions v0.3.30 [09f84164] HypothesisTests v0.11.8 [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 v1.8.0 [b964fa9f] LaTeXStrings v1.4.1 [2ab3a3ac] LogExpFunctions v1.0.1 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v2.0.1 [90014a1f] PDMats v0.11.41 ⌅ [69de0a69] Parsers v2.8.7 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.8 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.7 [91c51154] SentinelArrays v1.4.10 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.9.0 [10745b16] Statistics v1.11.4 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.13 [4c63d2b9] StatsFuns v2.2.1 ⌅ [892a3eda] StringManipulation v0.5.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.14.0 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.2+0 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.12.0 [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 v1.14.0 [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 v1.13.0 [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 v1.5.7+0 [deac9b47] LibCURL_jll v8.21.0+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.8+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 v1.70.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.0s Test Summary: | Pass Total Time openvcf | 4 4 3.8s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 3.5s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 4.8s ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 ┌ 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: 1:08:35 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 19.824494 seconds (6.87 M allocations: 464.955 MiB, 1.94% gc time, 96.32% compilation time: 4% of which was recompilation) 0.479560 seconds (1.36 M allocations: 111.044 MiB, 12.76% gc time, 24.74% compilation time) Progress: 0%| | ETA: 1:06:43 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 6.678104 seconds (2.28 M allocations: 170.799 MiB, 3.83% gc time, 88.72% compilation time) 0.679329 seconds (1.35 M allocations: 110.505 MiB, 1.07% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 33.4s 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 2.1s 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 1.3s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:13:47 Progress: 0%|▏ | ETA: 0:14:23 Progress: 0%|▏ | ETA: 0:13:41 Progress: 1%|▎ | ETA: 0:13:46 Progress: 1%|▎ | ETA: 0:13:31 Progress: 1%|▍ | ETA: 0:13:20 Progress: 1%|▍ | ETA: 0:13:17 Progress: 1%|▍ | ETA: 0:13:35 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| ETA: 0:12:49 Progress: 5%|██▎ | ETA: 0:12:47 Progress: 6%|██▎ | ETA: 0:12:47 Progress: 6%|██▍ | ETA: 0:12:45 Progress: 6%|██▍ | ETA: 0:12:43 Progress: 6%|██▌ | ETA: 0:12:41 Progress: 6%|██▌ | ETA: 0:12:41 Progress: 6%|██▌ | ETA: 0:12:40 Progress: 6%|██▋ | ETA: 0:12:38 Progress: 6%|██▋ | ETA: 0:12:38 Progress: 7%|██▊ | ETA: 0:12:36 Progress: 7%|██▊ | ETA: 0:12:34 Progress: 7%|██▉ | ETA: 0:12:31 Progress: 7%|██▉ | ETA: 0:12:30 Progress: 7%|██▉ | ETA: 0:12:28 Progress: 7%|███ | ETA: 0:12:25 Progress: 7%|███ | ETA: 0:12:25 Progress: 8%|███▏ | ETA: 0:12:23 Progress: 8%|███▏ | ETA: 0:12:22 Progress: 8%|███▎ | ETA: 0:12:19 Progress: 8%|███▎ | ETA: 0:12:20 Progress: 8%|███▍ | ETA: 0:12:17 Progress: 8%|███▍ | ETA: 0:12:15 Progress: 8%|███▌ | ETA: 0:12:13 Progress: 9%|███▌ | ETA: 0:12:11 Progress: 9%|███▌ | ETA: 0:12:10 Progress: 9%|███▋ | ETA: 0:12:08 Progress: 9%|███▋ | ETA: 0:12:08 Progress: 9%|███▊ | ETA: 0:12:06 Progress: 9%|███▊ | ETA: 0:12:04 Progress: 9%|███▉ | ETA: 0:12:04 Progress: 9%|███▉ | ETA: 0:12:03 Progress: 10%|███▉ | ETA: 0:12:01 Progress: 10%|████ | ETA: 0:12:00 Progress: 10%|████ | ETA: 0:12:01 Progress: 10%|████▏ | ETA: 0:11:59 Progress: 10%|████▏ | ETA: 0:11:58 Progress: 10%|████▎ | ETA: 0:11:57 Progress: 100%|█████████████████████████████████████████| Time: 0:01:22 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 14:54:02 Progress: 23%|█████████▎ | ETA: 0:04:35 Progress: 46%|██████████████████▋ | ETA: 0:01:37 Progress: 70%|████████████████████████████▌ | ETA: 0:00:36 Progress: 93%|██████████████████████████████████████▎ | ETA: 0:00:06 Progress: 100%|█████████████████████████████████████████| Time: 0:01:23 [ Info: 823 records are matched 177.661184 seconds (1.12 G allocations: 85.512 GiB, 7.94% gc time, 0.72% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:14:28 Progress: 0%|▏ | ETA: 0:13:44 Progress: 0%|▏ | ETA: 0:14:00 Progress: 1%|▎ | ETA: 0:13:39 Progress: 1%|▎ | ETA: 0:13:26 Progress: 1%|▍ | ETA: 0:13:16 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| ETA: 0:12:41 Progress: 5%|██ | ETA: 0:12:40 Progress: 5%|██▏ | ETA: 0:12:39 Progress: 5%|██▏ | ETA: 0:12:39 Progress: 5%|██▎ | ETA: 0:12:37 Progress: 5%|██▎ | ETA: 0:12:35 Progress: 6%|██▎ | ETA: 0:12:36 Progress: 6%|██▍ | ETA: 0:12:35 Progress: 6%|██▍ | ETA: 0:12:35 Progress: 6%|██▌ | ETA: 0:12:34 Progress: 6%|██▌ | ETA: 0:12:34 Progress: 6%|██▌ | ETA: 0:12:34 Progress: 6%|██▋ | ETA: 0:12:33 Progress: 6%|██▋ | ETA: 0:12:32 Progress: 7%|██▊ | ETA: 0:12:32 Progress: 7%|██▊ | ETA: 0:12:31 Progress: 7%|██▉ | ETA: 0:12:29 Progress: 7%|██▉ | ETA: 0:12:28 Progress: 7%|██▉ | ETA: 0:12:26 Progress: 7%|███ | ETA: 0:12:24 Progress: 7%|███ | ETA: 0:12:22 Progress: 8%|███▏ | ETA: 0:12:22 Progress: 8%|███▏ | ETA: 0:12:20 Progress: 8%|███▎ | ETA: 0:12:19 Progress: 8%|███▎ | ETA: 0:12:18 Progress: 8%|███▍ | ETA: 0:12:17 Progress: 8%|███▍ | ETA: 0:12:16 Progress: 8%|███▍ | ETA: 0:12:15 Progress: 8%|███▌ | ETA: 0:12:15 Progress: 9%|███▌ | ETA: 0:12:13 Progress: 9%|███▋ | ETA: 0:12:12 Progress: 9%|███▋ | ETA: 0:12:13 Progress: 9%|███▋ | ETA: 0:12:12 Progress: 9%|███▊ | ETA: 0:12:10 Progress: 9%|███▊ | ETA: 0:12:09 Progress: 9%|███▉ | ETA: 0:12:08 Progress: 9%|███▉ | ETA: 0:12:07 Progress: 10%|████ | ETA: 0:12:06 Progress: 10%|████ | ETA: 0:12:04 Progress: 10%|████ | ETA: 0:12:04 Progress: 10%|████▏ | ETA: 0:12:03 Progress: 10%|████▏ | ETA: 0:12:02 Progress: 10%|████▎ | ETA: 0:12:01 Progress: 100%|█████████████████████████████████████████| Time: 0:01:23 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 15:06:04 Progress: 21%|████████▊ | ETA: 0:05:00 Progress: 44%|██████████████████▏ | ETA: 0:01:44 Progress: 70%|████████████████████████████▋ | ETA: 0:00:36 Progress: 95%|██████████████████████████████████████▉ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:01:24 [ Info: 0 records are matched 178.708067 seconds (1.12 G allocations: 85.492 GiB, 8.08% gc time, 0.49% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 9m00.9s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 15:00:08 Progress: 22%|█████████ | ETA: 0:04:47 Progress: 43%|█████████████████▊ | ETA: 0:01:47 Progress: 69%|████████████████████████████▎ | ETA: 0:00:37 Progress: 94%|██████████████████████████████████████▋ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:01:24 [ Info: 833 records are matched 94.965789 seconds (569.62 M allocations: 43.521 GiB, 7.74% gc time, 0.69% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 15:09:51 Progress: 20%|████████▍ | ETA: 0:05:20 Progress: 44%|█████████████████▉ | ETA: 0:01:47 Progress: 67%|███████████████████████████▍ | ETA: 0:00:42 Progress: 91%|█████████████████████████████████████▍ | ETA: 0:00:08 Progress: 100%|█████████████████████████████████████████| Time: 0:01:25 [ Info: 493 records are matched 95.659656 seconds (569.61 M allocations: 43.521 GiB, 7.82% gc time, 0.66% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 14:35:41 Progress: 22%|████████▉ | ETA: 0:04:45 Progress: 45%|██████████████████▋ | ETA: 0:01:36 Progress: 69%|████████████████████████████▎ | ETA: 0:00:36 Progress: 94%|██████████████████████████████████████▊ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:01:21 [ Info: 0 records are matched 92.474027 seconds (569.61 M allocations: 43.521 GiB, 7.74% gc time, 0.68% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 4m44.7s 1.233086 seconds (1.14 M allocations: 67.678 MiB, 1.72% gc time, 74.92% compilation time) 1.142107 seconds (1.04 M allocations: 64.262 MiB, 73.33% compilation time) 1.145675 seconds (1.04 M allocations: 63.197 MiB, 1.84% gc time, 69.51% compilation time) 0.409307 seconds (172.84 k allocations: 10.705 MiB, 99.94% compilation time) 0.014977 seconds (5.76 k allocations: 376.758 KiB, 95.68% compilation time) 0.012401 seconds (2.61 k allocations: 165.492 KiB, 95.29% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.7s 1.076243 seconds (932.73 k allocations: 56.416 MiB, 67.37% compilation time) 0.925832 seconds (798.92 k allocations: 50.369 MiB, 3.18% gc time, 59.10% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.4s Test Summary: | Pass Total Time convert_ds | 5 5 1.4s 0.287060 seconds (523.22 k allocations: 30.573 MiB, 47.92% gc time, 8.29% compilation time) 0.631453 seconds (624.15 k allocations: 37.468 MiB, 79.21% 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 0.124158 seconds (520.01 k allocations: 32.143 MiB) 0.509038 seconds (580.70 k allocations: 36.159 MiB, 3.59% gc time, 71.18% 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:784 [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:2247 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.188756 seconds (1.30 M allocations: 54.160 MiB, 6.80% compilation time) 0.573207 seconds (1.41 M allocations: 61.871 MiB, 5.19% gc time, 75.05% 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 20.6s RNG of the outermost testset: Xoshiro(0xde91d7791c75a235, 0x7516721bf67bda07, 0x9096cef1db7c3661, 0x9d059d9b54284229, 0x5bee87c596700f4e) 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 954.27s 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:3283 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1399.46s: package has test failures