Package evaluation to test VCFTools on Julia 1.14.0-DEV.2637 (b1f508acef*) started at 2026-07-12T20:50:43.018 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.89s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed CommonSolve ───────────── v0.2.11 Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed DataStructures ────────── v0.19.5 Installed DelimitedFiles ────────── v1.9.1 Installed MacroTools ────────────── v0.5.16 Installed FillArrays ────────────── v1.16.0 Installed VCFTools ──────────────── v0.2.10 Installed HypergeometricFunctions ─ v0.3.29 Installed OrderedCollections ────── v1.8.2 Installed StatsBase ─────────────── v0.34.12 Installed ConstructionBase ──────── v1.6.0 Installed CodecZlib ─────────────── v0.7.8 Installed AliasTables ───────────── v1.1.3 Installed TranscodingStreams ────── v0.11.3 Installed DataAPI ───────────────── v1.16.0 Installed Statistics ────────────── v1.11.1 Installed HypothesisTests ───────── v0.11.8 Installed Combinatorics ─────────── v1.1.0 Installed PrecompileTools ───────── v1.3.4 Installed StatsAPI ──────────────── v1.8.0 Installed IrrationalConstants ───── v0.2.6 Installed ProgressMeter ─────────── v1.11.0 Installed LogExpFunctions ───────── v1.0.1 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed BufferedStreams ───────── v1.2.2 Installed Roots ─────────────────── v3.0.4 Installed QuadGK ────────────────── v2.11.3 Installed Gamma ─────────────────── v1.1.0 Installed Distributions ─────────── v0.25.129 Installed StatsFuns ─────────────── v2.2.0 Installed SpecialFunctions ──────── v2.8.0 Installed Rmath ─────────────────── v0.9.0 Installed PtrArrays ─────────────── v1.4.0 Installed Reexport ──────────────── v1.2.2 Installed Missings ──────────────── v1.2.0 Installed BioGenerics ───────────── v0.1.5 Installed SortingAlgorithms ─────── v1.2.3 Installed InverseFunctions ──────── v0.1.17 Installed JLLWrappers ───────────── v1.8.0 Installed Preferences ───────────── v1.5.2 Installed PDMats ────────────────── v0.11.40 Installed Accessors ─────────────── v0.1.45 Installed DocStringExtensions ───── v0.9.5 Installed BGZFStreams ───────────── v0.3.2 Installed Automa ────────────────── v1.2.0 Installed VariantCallFormat ─────── v0.5.9 Installing 2 artifacts Installed artifact OpenSpecFun 105.4 KiB Installed artifact Rmath 111.5 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 v0.7.8 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.11 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.5 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.129 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [a0844989] + Gamma v1.1.0 [34004b35] + HypergeometricFunctions v0.3.29 [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 v1.8.2 [90014a1f] + PDMats v0.11.40 [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 v3.0.4 [a2af1166] + SortingAlgorithms v1.2.3 [276daf66] + SpecialFunctions v2.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [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 v1.14.0 [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 v1.5.5+2 [4536629a] + OpenBLAS_jll v0.3.33+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 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 8.62s ################################################################################ # 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... 7.0 s ✓ MacroTools 1.8 s ✓ InlineStrings 0.5 s ✓ Reexport 0.8 s ✓ Statistics 0.6 s ✓ DataAPI 0.8 s ✓ ConstructionBase 2.0 s ✓ IrrationalConstants 0.5 s ✓ DataValueInterfaces 0.6 s ✓ StatsAPI 1.1 s ✓ OrderedCollections 0.6 s ✓ InvertedIndices 0.9 s ✓ InverseFunctions 0.5 s ✓ CompositionsBase 1.9 s ✓ DocStringExtensions 2.3 s ✓ Combinatorics 1.0 s ✓ Gamma 0.9 s ✓ WorkerUtilities 2.1 s ✓ FillArrays 1.3 s ✓ BufferedStreams 0.5 s ✓ PtrArrays 0.5 s ✓ CommonSolve 0.9 s ✓ TranscodingStreams 0.5 s ✓ IteratorInterfaceExtensions 0.6 s ✓ LaTeXStrings 1.9 s ✓ Crayons 0.7 s ✓ DelimitedFiles 2.0 s ✓ PDMats 2.1 s ✓ ProgressMeter 2.1 s ✓ SentinelArrays 0.8 s ✓ Compat 1.4 s ✓ Preferences 1.6 s ✓ Statistics → SparseArraysExt 0.7 s ✓ Missings 0.7 s ✓ PooledArrays 0.5 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3.8 s ✓ DataStructures 1.4 s ✓ InverseFunctions → InverseFunctionsTestExt 1.2 s ✓ InverseFunctions → InverseFunctionsDatesExt 0.5 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.1 s ✓ LogExpFunctions 1.7 s ✓ HypergeometricFunctions 1.8 s ✓ FillArrays → FillArraysSparseArraysExt 0.9 s ✓ FillArrays → FillArraysStatisticsExt 0.7 s ✓ AliasTables 0.7 s ✓ BioGenerics 1.2 s ✓ CodecZlib 0.6 s ✓ TableTraits 1.8 s ✓ FillArrays → FillArraysPDMatsExt 0.7 s ✓ Compat → CompatLinearAlgebraExt 1.8 s ✓ JLLWrappers 1.1 s ✓ PrecompileTools 0.8 s ✓ SortingAlgorithms 2.0 s ✓ QuadGK 3.9 s ✓ Accessors 0.5 s ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 0.6 s ✓ BGZFStreams 1.1 s ✓ Tables 1.4 s ✓ FilePathsBase 1.3 s ✓ Rmath_jll 1.1 s ✓ OpenSpecFun_jll 18.9 s ✓ Automa 3.5 s ✓ StringManipulation 9.7 s ✓ Parsers 4.7 s ✓ StatsBase 2.4 s ✓ Accessors → LinearAlgebraExt 1.6 s ✓ Accessors → TestExt 2.6 s ✓ FilePathsBase → FilePathsBaseTestExt 0.8 s ✓ FilePathsBase → FilePathsBaseMmapExt 1.9 s ✓ Rmath 5.5 s ✓ SpecialFunctions [ Info: Compiling VCF parser... 15.6 s ✓ VariantCallFormat 44.3 s ✓ PrettyTables 0.8 s ✓ InlineStrings → ParsersExt 2.2 s ✓ PDMats → StatsBaseExt 5.6 s ✓ Roots 2.7 s ✓ StatsFuns 77.1 s ✓ DataFrames 2.1 s ✓ WeakRefStrings 1.6 s ✓ StatsFuns → StatsFunsInverseFunctionsExt 22.5 s ✓ CSV 10.4 s ✓ Distributions 4.5 s ✓ Distributions → DistributionsTestExt 4.8 s ✓ HypothesisTests 5.5 s ✓ VCFTools 84 dependencies successfully precompiled in 330 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 348.96s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_u1TqPo/Project.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.129 [09f84164] HypothesisTests v0.11.8 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 [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_u1TqPo/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 v0.10.16 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.11 [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 v1.8.2 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.129 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [a0844989] Gamma v1.1.0 [34004b35] HypergeometricFunctions v0.3.29 [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 v1.4.0 [2ab3a3ac] LogExpFunctions v1.0.1 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.40 [69de0a69] Parsers v2.8.6 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.0 [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 v3.0.4 [91c51154] SentinelArrays v1.4.10 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.8.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.2.0 [892a3eda] StringManipulation v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.13.0 [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 v0.5.1+0 [0dad84c5] ArgTools v1.2.0 [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 v1.14.0 [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 v1.5.5+2 [deac9b47] LibCURL_jll v8.21.0+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.7+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 v1.69.0+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 2.6s Test Summary: | Pass Total Time openvcf | 4 4 2.8s 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 4.3s ┌ 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: 1:04:23 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 20.382167 seconds (6.41 M allocations: 437.022 MiB, 0.76% gc time, 96.07% compilation time: 4% of which was recompilation) 0.401579 seconds (1.35 M allocations: 110.655 MiB, 14.98% gc time, 16.78% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 1:02:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:06 6.125558 seconds (2.23 M allocations: 168.339 MiB, 2.73% gc time, 90.83% compilation time: <1% of which was recompilation) 0.575580 seconds (1.35 M allocations: 110.915 MiB, 2.05% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 32.6s 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 1.9s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.2s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.2s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.2s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:12:28 Progress: 0%|▏ | ETA: 0:13:14 Progress: 0%|▏ | ETA: 0:12:50 Progress: 1%|▎ | ETA: 0:13:08 Progress: 1%|▎ | ETA: 0:12:55 Progress: 1%|▍ | ETA: 0:12:46 Progress: 1%|▍ | ETA: 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ETA: 0:11:21 Progress: 10%|████ | ETA: 0:11:20 Progress: 10%|████▏ | ETA: 0:11:19 Progress: 10%|████▏ | ETA: 0:11:18 Progress: 10%|████▎ | ETA: 0:11:17 Progress: 100%|█████████████████████████████████████████| Time: 0:01:17 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 14:14:49 Progress: 20%|████████▎ | ETA: 0:05:06 Progress: 43%|█████████████████▊ | ETA: 0:01:42 Progress: 66%|███████████████████████████▏ | ETA: 0:00:40 Progress: 90%|█████████████████████████████████████ | ETA: 0:00:09 Progress: 100%|█████████████████████████████████████████| Time: 0:01:20 [ Info: 823 records are matched 169.569094 seconds (1.12 G allocations: 85.512 GiB, 8.27% gc time, 0.90% compilation time: <1% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:12:20 Progress: 0%|▏ | ETA: 0:12:46 Progress: 0%|▏ | ETA: 0:12:29 Progress: 1%|▎ | ETA: 0:12:21 Progress: 1%|▎ | ETA: 0:12:31 Progress: 1%|▍ | ETA: 0:12:25 Progress: 1%|▍ | ETA: 0:12:21 Progress: 1%|▌ | 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Progress: 10%|████ | ETA: 0:12:04 Progress: 10%|████ | ETA: 0:12:02 Progress: 10%|████ | ETA: 0:12:02 Progress: 10%|████▏ | ETA: 0:12:01 Progress: 10%|████▏ | ETA: 0:11:59 Progress: 10%|████▎ | ETA: 0:12:00 Progress: 100%|█████████████████████████████████████████| Time: 0:01:22 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 15:05:24 Progress: 21%|████████▍ | ETA: 0:05:15 Progress: 42%|█████████████████▍ | ETA: 0:01:52 Progress: 66%|███████████████████████████▏ | ETA: 0:00:43 Progress: 90%|████████████████████████████████████▊ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:01:24 [ Info: 0 records are matched 179.004623 seconds (1.12 G allocations: 85.492 GiB, 7.61% gc time, 0.59% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 8m48.9s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 15:02:57 Progress: 19%|████████ | ETA: 0:05:35 Progress: 41%|████████████████▉ | ETA: 0:01:57 Progress: 63%|█████████████████████████▉ | ETA: 0:00:49 Progress: 87%|███████████████████████████████████▋ | ETA: 0:00:13 Progress: 100%|█████████████████████████████████████████| Time: 0:01:24 [ Info: 833 records are matched 95.497840 seconds (569.60 M allocations: 43.521 GiB, 6.85% gc time, 0.70% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 15:04:13 Progress: 22%|█████████▏ | ETA: 0:04:42 Progress: 44%|██████████████████▏ | ETA: 0:01:44 Progress: 68%|████████████████████████████ | ETA: 0:00:38 Progress: 93%|██████████████████████████████████████ | ETA: 0:00:07 Progress: 100%|█████████████████████████████████████████| Time: 0:01:24 [ Info: 493 records are matched 95.584091 seconds (569.60 M allocations: 43.521 GiB, 6.83% gc time, 0.70% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 15:07:13 Progress: 23%|█████████▌ | ETA: 0:04:30 Progress: 46%|██████████████████▉ | ETA: 0:01:37 Progress: 71%|█████████████████████████████▏ | ETA: 0:00:34 Progress: 96%|███████████████████████████████████████▏ | ETA: 0:00:04 Progress: 100%|█████████████████████████████████████████| Time: 0:01:24 [ Info: 0 records are matched 95.574236 seconds (569.59 M allocations: 43.520 GiB, 6.87% gc time, 0.69% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 4m48.5s 1.241608 seconds (1.11 M allocations: 66.036 MiB, 1.25% gc time, 76.17% compilation time) 1.105863 seconds (1.02 M allocations: 63.094 MiB, 1.44% gc time, 72.55% compilation time) 1.082286 seconds (1.02 M allocations: 62.064 MiB, 72.62% compilation time) 0.461597 seconds (166.47 k allocations: 10.340 MiB, 99.95% compilation time) 0.013330 seconds (5.45 k allocations: 365.211 KiB, 94.86% compilation time) 0.010736 seconds (2.60 k allocations: 164.945 KiB, 94.19% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.7s 1.133420 seconds (921.89 k allocations: 55.704 MiB, 2.75% gc time, 75.44% compilation time) 1.050160 seconds (783.10 k allocations: 49.517 MiB, 73.12% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.8s Test Summary: | Pass Total Time convert_ds | 5 5 1.3s 0.202073 seconds (523.16 k allocations: 30.569 MiB, 7.87% gc time, 15.86% compilation time) 0.656519 seconds (618.36 k allocations: 37.180 MiB, 76.87% 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 0.148434 seconds (520.01 k allocations: 32.143 MiB) 0.644414 seconds (576.91 k allocations: 35.965 MiB, 76.66% 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:2246 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.209657 seconds (1.30 M allocations: 54.159 MiB, 5.22% compilation time) 0.808030 seconds (1.41 M allocations: 61.669 MiB, 2.68% gc time, 73.60% 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 22.1s RNG of the outermost testset: Xoshiro(0xc8a7ee506fd0973a, 0xf39ec67fb3de8c16, 0xd557ab930deb8ecc, 0xf965c35e97ef4c5c, 0xa002f344f8911bfc) 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 949.11s 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:3247 [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 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1399.19s: package has test failures