Package evaluation to test VCFTools on Julia 1.14.0-DEV.2232 (ecceaba1c5*) started at 2026-05-27T06:40:04.187 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.56s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed DelimitedFiles ────────── v1.9.1 Installed CompositionsBase ──────── v0.1.2 Installed FillArrays ────────────── v1.16.0 Installed CommonSolve ───────────── v0.2.7 Installed DataStructures ────────── v0.19.4 Installed MacroTools ────────────── v0.5.16 Installed ConstructionBase ──────── v1.6.0 Installed VCFTools ──────────────── v0.2.10 Installed AliasTables ───────────── v1.1.3 Installed CodecZlib ─────────────── v0.7.8 Installed StatsBase ─────────────── v0.34.10 Installed OrderedCollections ────── v1.8.1 Installed Combinatorics ─────────── v1.1.0 Installed HypergeometricFunctions ─ v0.3.28 Installed TranscodingStreams ────── v0.11.3 Installed SIMD ──────────────────── v3.7.2 Installed HypothesisTests ───────── v0.11.7 Installed DataAPI ───────────────── v1.16.0 Installed Statistics ────────────── v1.11.1 Installed StatsAPI ──────────────── v1.8.0 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed LogExpFunctions ───────── v0.3.29 Installed ProgressMeter ─────────── v1.11.0 Installed IrrationalConstants ───── v0.2.6 Installed QuadGK ────────────────── v2.11.3 Installed PrecompileTools ───────── v1.3.4 Installed BufferedStreams ───────── v1.2.2 Installed Rmath ─────────────────── v0.9.0 Installed Roots ─────────────────── v3.0.0 Installed BioGenerics ───────────── v0.1.5 Installed StatsFuns ─────────────── v1.5.2 Installed PtrArrays ─────────────── v1.4.0 Installed Reexport ──────────────── v1.2.2 Installed InverseFunctions ──────── v0.1.17 Installed Preferences ───────────── v1.5.2 Installed Missings ──────────────── v1.2.0 Installed SpecialFunctions ──────── v2.7.2 Installed Distributions ─────────── v0.25.125 Installed PDMats ────────────────── v0.11.37 Installed SortingAlgorithms ─────── v1.2.2 Installed Automa ────────────────── v1.1.0 Installed JLLWrappers ───────────── v1.8.0 Installed DocStringExtensions ───── v0.9.5 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.9 Installed Accessors ─────────────── v0.1.44 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 v0.1.44 [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 v0.2.7 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.4 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.125 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.7 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.8.0 [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 [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 v3.0.0 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.2 [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 v1.13.0 [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 v1.5.1+0 [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 Installation completed after 8.99s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 3.9 s ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 3.6 s ✓ MacroTools 1.3 s ✓ InlineStrings 0.4 s ✓ Reexport 0.7 s ✓ Statistics 0.5 s ✓ DataAPI 0.8 s ✓ ConstructionBase 1.7 s ✓ IrrationalConstants 0.4 s ✓ DataValueInterfaces 0.5 s ✓ StatsAPI 1.0 s ✓ OrderedCollections 0.5 s ✓ InvertedIndices 0.6 s ✓ InverseFunctions 0.4 s ✓ CompositionsBase 0.8 s ✓ DocStringExtensions 1.6 s ✓ Combinatorics 0.7 s ✓ WorkerUtilities 2.0 s ✓ FillArrays 0.7 s ✓ BufferedStreams 0.4 s ✓ PtrArrays 0.4 s ✓ CommonSolve 1.0 s ✓ TranscodingStreams 0.4 s ✓ IteratorInterfaceExtensions 0.5 s ✓ LaTeXStrings 1.6 s ✓ Crayons 0.6 s ✓ DelimitedFiles 2.4 s ✓ PDMats 2.0 s ✓ ProgressMeter 1.9 s ✓ SentinelArrays 0.8 s ✓ Compat 1.1 s ✓ Preferences 1.8 s ✓ Statistics → SparseArraysExt 0.6 s ✓ Missings 0.7 s ✓ PooledArrays 0.4 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3.4 s ✓ DataStructures 1.5 s ✓ InverseFunctions → InverseFunctionsTestExt 0.9 s ✓ InverseFunctions → InverseFunctionsDatesExt 0.4 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.0 s ✓ LogExpFunctions 2.1 s ✓ FillArrays → FillArraysSparseArraysExt 0.8 s ✓ FillArrays → FillArraysStatisticsExt 0.6 s ✓ AliasTables 0.6 s ✓ BioGenerics 0.6 s ✓ CodecZlib 0.4 s ✓ TableTraits 2.0 s ✓ FillArrays → FillArraysPDMatsExt 0.5 s ✓ Compat → CompatLinearAlgebraExt 1.9 s ✓ JLLWrappers 1.6 s ✓ PrecompileTools 0.9 s ✓ SortingAlgorithms 1.9 s ✓ QuadGK 4.7 s ✓ Accessors 0.5 s ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 0.7 s ✓ BGZFStreams 1.5 s ✓ Tables 1.6 s ✓ FilePathsBase 1.5 s ✓ Rmath_jll 1.8 s ✓ OpenSpecFun_jll 3.8 s ✓ StringManipulation 15.1 s ✓ SIMD 16.4 s ✓ Parsers 4.4 s ✓ StatsBase 2.0 s ✓ Accessors → LinearAlgebraExt 1.7 s ✓ Accessors → TestExt 2.7 s ✓ FilePathsBase → FilePathsBaseTestExt 0.8 s ✓ FilePathsBase → FilePathsBaseMmapExt 1.5 s ✓ Rmath 5.1 s ✓ SpecialFunctions 42.3 s ✓ PrettyTables 17.3 s ✓ Automa 0.9 s ✓ InlineStrings → ParsersExt 1.9 s ✓ PDMats → StatsBaseExt 6.5 s ✓ Roots 2.2 s ✓ HypergeometricFunctions 85.7 s ✓ DataFrames [ Info: Compiling VCF parser... 15.4 s ✓ VariantCallFormat 2.9 s ✓ WeakRefStrings 3.1 s ✓ StatsFuns 25.1 s ✓ CSV 1.0 s ✓ StatsFuns → StatsFunsInverseFunctionsExt 10.5 s ✓ Distributions 4.2 s ✓ Distributions → DistributionsTestExt 5.0 s ✓ HypothesisTests 5.4 s ✓ VCFTools 84 dependencies successfully precompiled in 351 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 382.26s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_HxkRCX/Project.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.125 [09f84164] HypothesisTests v0.11.7 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.7.2 [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_HxkRCX/Manifest.toml` [7d9f7c33] Accessors v0.1.44 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.7 [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 v0.19.4 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.125 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.7 [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 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 v2.8.4 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [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 v3.0.0 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.10 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.2 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.3 [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 v1.13.0 [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 v1.5.1+0 [deac9b47] LibCURL_jll v8.20.0+1 [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 v3.5.6+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 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 2.5s Test Summary: | Pass Total Time openvcf | 4 4 2.1s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.8s ┌ 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: 0:42:10 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 15.139636 seconds (8.99 M allocations: 544.547 MiB, 2.73% gc time, 94.00% compilation time: 14% of which was recompilation) 0.372095 seconds (2.37 M allocations: 141.300 MiB, 6.61% gc time, 15.85% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:38:29 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.824805 seconds (3.95 M allocations: 239.950 MiB, 1.34% gc time, 89.15% compilation time) 0.437481 seconds (2.37 M allocations: 141.301 MiB, 5.89% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.3s 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 1.9s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 1.9s 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 1.0s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:21:17 Progress: 0%|▏ | ETA: 0:18:44 Progress: 0%|▏ | ETA: 0:18:10 Progress: 0%|▏ | ETA: 0:17:56 Progress: 0%|▎ | ETA: 0:18:07 Progress: 1%|▎ | ETA: 0:17:55 Progress: 1%|▎ | ETA: 0:17:43 Progress: 1%|▍ | ETA: 0:17:37 Progress: 1%|▍ | ETA: 0:17:57 Progress: 1%|▍ | ETA: 0:17:50 Progress: 1%|▍ | ETA: 0:17:44 Progress: 1%|▌ | ETA: 0:17:39 Progress: 1%|▌ | ETA: 0:17:48 Progress: 1%|▌ | ETA: 0:17:46 Progress: 1%|▋ | ETA: 0:17:42 Progress: 2%|▋ | ETA: 0:17:39 Progress: 2%|▋ | ETA: 0:17:35 Progress: 2%|▊ | ETA: 0:17:45 Progress: 2%|▊ | ETA: 0:17:39 Progress: 2%|▊ | ETA: 0:17:36 Progress: 2%|▉ | ETA: 0:17:33 Progress: 2%|▉ | ETA: 0:17:37 Progress: 2%|▉ | ETA: 0:17:36 Progress: 2%|█ | ETA: 0:17:32 Progress: 2%|█ | ETA: 0:17:29 Progress: 3%|█ | ETA: 0:17:27 Progress: 3%|█▏ | ETA: 0:17:32 Progress: 3%|█▏ | ETA: 0:17:28 Progress: 3%|█▏ | ETA: 0:17:26 Progress: 3%|█▎ | ETA: 0:17:24 Progress: 3%|█▎ | ETA: 0:17:25 Progress: 3%|█▎ | ETA: 0:17:23 Progress: 3%|█▍ | ETA: 0:17:20 Progress: 3%|█▍ | ETA: 0:17:17 Progress: 3%|█▍ | ETA: 0:17:15 Progress: 4%|█▌ | ETA: 0:17:17 Progress: 4%|█▌ | ETA: 0:17:15 Progress: 4%|█▌ | ETA: 0:17:14 Progress: 4%|█▌ | ETA: 0:17:11 Progress: 4%|█▋ | ETA: 0:17:13 Progress: 4%|█▋ | ETA: 0:17:12 Progress: 4%|█▋ | ETA: 0:17:10 Progress: 4%|█▊ | ETA: 0:17:08 Progress: 4%|█▊ | ETA: 0:16:58 Progress: 4%|█▉ | ETA: 0:16:54 Progress: 5%|█▉ | ETA: 0:16:43 Progress: 5%|█▉ | ETA: 0:16:31 Progress: 5%|██ | ETA: 0:16:21 Progress: 5%|██ | ETA: 0:16:11 Progress: 5%|██▏ | ETA: 0:16:01 Progress: 5%|██▏ | ETA: 0:15:54 Progress: 5%|██▎ | ETA: 0:15:45 Progress: 6%|██▎ | ETA: 0:15:35 Progress: 6%|██▍ | ETA: 0:15:28 Progress: 6%|██▍ | ETA: 0:15:20 Progress: 6%|██▌ | ETA: 0:15:12 Progress: 6%|██▌ | ETA: 0:15:07 Progress: 6%|██▋ | ETA: 0:15:00 Progress: 6%|██▋ | ETA: 0:14:52 Progress: 7%|██▊ | ETA: 0:14:48 Progress: 7%|██▊ | ETA: 0:14:42 Progress: 7%|██▉ | ETA: 0:14:35 Progress: 7%|██▉ | ETA: 0:14:30 Progress: 7%|███ | ETA: 0:14:24 Progress: 7%|███ | ETA: 0:14:20 Progress: 7%|███▏ | ETA: 0:14:16 Progress: 8%|███▏ | ETA: 0:14:11 Progress: 8%|███▏ | ETA: 0:14:06 Progress: 8%|███▎ | ETA: 0:14:03 Progress: 8%|███▎ | ETA: 0:13:57 Progress: 8%|███▍ | ETA: 0:13:54 Progress: 8%|███▍ | ETA: 0:13:51 Progress: 8%|███▌ | ETA: 0:13:47 Progress: 9%|███▌ | ETA: 0:13:43 Progress: 9%|███▋ | ETA: 0:13:38 Progress: 9%|███▋ | ETA: 0:13:35 Progress: 9%|███▊ | ETA: 0:13:31 Progress: 9%|███▊ | ETA: 0:13:27 Progress: 9%|███▉ | ETA: 0:13:25 Progress: 9%|███▉ | ETA: 0:13:21 Progress: 10%|████ | ETA: 0:13:19 Progress: 10%|████ | ETA: 0:13:21 Progress: 10%|████ | ETA: 0:13:20 Progress: 10%|████▏ | ETA: 0:13:21 Progress: 10%|████▏ | ETA: 0:13:21 Progress: 10%|████▏ | ETA: 0:13:22 Progress: 10%|████▎ | ETA: 0:13:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:32 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:23:20 Progress: 16%|██████▍ | ETA: 0:09:22 Progress: 37%|███████████████ | ETA: 0:03:02 Progress: 57%|███████████████████████▌ | ETA: 0:01:19 Progress: 78%|███████████████████████████████▊ | ETA: 0:00:31 Progress: 99%|████████████████████████████████████████▉| ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: 823 records are matched 211.500378 seconds (2.01 G allocations: 106.068 GiB, 8.65% gc time, 0.64% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:22 Progress: 0%|▏ | ETA: 0:17:10 Progress: 0%|▏ | ETA: 0:18:00 Progress: 0%|▏ | ETA: 0:17:52 Progress: 0%|▎ | ETA: 0:17:38 Progress: 1%|▎ | ETA: 0:16:59 Progress: 1%|▎ | ETA: 0:17:04 Progress: 1%|▍ | ETA: 0:17:03 Progress: 1%|▍ | ETA: 0:17:00 Progress: 1%|▍ | ETA: 0:16:52 Progress: 1%|▌ | ETA: 0:16:45 Progress: 1%|▌ | ETA: 0:16:52 Progress: 1%|▌ | ETA: 0:16:52 Progress: 1%|▋ | ETA: 0:16:50 Progress: 2%|▋ | ETA: 0:16:49 Progress: 2%|▋ | ETA: 0:16:58 Progress: 2%|▊ | ETA: 0:16:55 Progress: 2%|▊ | ETA: 0:16:53 Progress: 2%|▊ | ETA: 0:16:52 Progress: 2%|▉ | ETA: 0:17:00 Progress: 2%|▉ | ETA: 0:17:00 Progress: 2%|▉ | ETA: 0:16:58 Progress: 2%|█ | ETA: 0:16:57 Progress: 2%|█ | ETA: 0:16:57 Progress: 2%|█ | ETA: 0:17:01 Progress: 3%|█ | ETA: 0:17:01 Progress: 3%|█▏ | ETA: 0:17:00 Progress: 3%|█▏ | ETA: 0:16:58 Progress: 3%|█▏ | ETA: 0:17:03 Progress: 3%|█▎ | ETA: 0:17:02 Progress: 3%|█▎ | ETA: 0:17:00 Progress: 3%|█▎ | ETA: 0:16:58 Progress: 3%|█▍ | ETA: 0:16:56 Progress: 3%|█▍ | ETA: 0:17:00 Progress: 3%|█▍ | ETA: 0:16:55 Progress: 4%|█▌ | ETA: 0:16:44 Progress: 4%|█▌ | ETA: 0:16:40 Progress: 4%|█▋ | ETA: 0:16:42 Progress: 4%|█▋ | ETA: 0:16:40 Progress: 4%|█▋ | ETA: 0:16:38 Progress: 4%|█▊ | ETA: 0:16:35 Progress: 4%|█▊ | ETA: 0:16:38 Progress: 4%|█▊ | ETA: 0:16:37 Progress: 4%|█▉ | ETA: 0:16:34 Progress: 5%|█▉ | ETA: 0:16:32 Progress: 5%|█▉ | ETA: 0:16:33 Progress: 5%|██ | ETA: 0:16:32 Progress: 5%|██ | ETA: 0:16:31 Progress: 5%|██ | ETA: 0:16:29 Progress: 5%|██▏ | ETA: 0:16:28 Progress: 5%|██▏ | ETA: 0:16:29 Progress: 5%|██▏ | ETA: 0:16:28 Progress: 5%|██▎ | ETA: 0:16:27 Progress: 5%|██▎ | ETA: 0:16:26 Progress: 6%|██▎ | ETA: 0:16:27 Progress: 6%|██▎ | ETA: 0:16:26 Progress: 6%|██▍ | ETA: 0:16:24 Progress: 6%|██▍ | ETA: 0:16:23 Progress: 6%|██▍ | ETA: 0:16:22 Progress: 6%|██▌ | ETA: 0:16:22 Progress: 6%|██▌ | ETA: 0:16:20 Progress: 6%|██▌ | ETA: 0:16:18 Progress: 6%|██▋ | ETA: 0:16:16 Progress: 6%|██▋ | ETA: 0:16:16 Progress: 7%|██▋ | ETA: 0:16:15 Progress: 7%|██▊ | ETA: 0:16:13 Progress: 7%|██▊ | ETA: 0:16:11 Progress: 7%|██▊ | ETA: 0:16:09 Progress: 7%|██▉ | ETA: 0:16:10 Progress: 7%|██▉ | ETA: 0:16:09 Progress: 7%|██▉ | ETA: 0:16:08 Progress: 7%|███ | ETA: 0:16:07 Progress: 7%|███ | ETA: 0:16:07 Progress: 7%|███ | ETA: 0:16:06 Progress: 8%|███▏ | ETA: 0:16:04 Progress: 8%|███▏ | ETA: 0:16:02 Progress: 8%|███▏ | ETA: 0:16:00 Progress: 8%|███▎ | ETA: 0:16:00 Progress: 8%|███▎ | ETA: 0:15:58 Progress: 8%|███▎ | ETA: 0:15:57 Progress: 8%|███▍ | ETA: 0:15:55 Progress: 8%|███▍ | ETA: 0:15:55 Progress: 8%|███▍ | ETA: 0:15:54 Progress: 8%|███▌ | ETA: 0:15:53 Progress: 9%|███▌ | ETA: 0:15:51 Progress: 9%|███▌ | ETA: 0:15:50 Progress: 9%|███▋ | ETA: 0:15:51 Progress: 9%|███▋ | ETA: 0:15:50 Progress: 9%|███▋ | ETA: 0:15:48 Progress: 9%|███▊ | ETA: 0:15:47 Progress: 9%|███▊ | ETA: 0:15:47 Progress: 9%|███▊ | ETA: 0:15:46 Progress: 9%|███▉ | ETA: 0:15:44 Progress: 9%|███▉ | ETA: 0:15:43 Progress: 10%|███▉ | ETA: 0:15:43 Progress: 10%|████ | ETA: 0:15:42 Progress: 10%|████ | ETA: 0:15:41 Progress: 10%|████ | ETA: 0:15:39 Progress: 10%|████▏ | ETA: 0:15:38 Progress: 10%|████▏ | ETA: 0:15:38 Progress: 10%|████▏ | ETA: 0:15:37 Progress: 10%|████▎ | ETA: 0:15:35 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:07:39 Progress: 17%|███████ | ETA: 0:08:44 Progress: 37%|███████████████▏ | ETA: 0:03:06 Progress: 59%|████████████████████████▍ | ETA: 0:01:15 Progress: 78%|████████████████████████████████▏ | ETA: 0:00:31 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 488 records are matched 230.409866 seconds (2.01 G allocations: 106.050 GiB, 8.17% gc time, 0.44% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:12 Progress: 0%|▏ | ETA: 0:17:54 Progress: 0%|▏ | ETA: 0:17:05 Progress: 0%|▏ | ETA: 0:16:26 Progress: 1%|▎ | ETA: 0:16:59 Progress: 1%|▎ | ETA: 0:16:54 Progress: 1%|▎ | ETA: 0:16:52 Progress: 1%|▍ | ETA: 0:16:52 Progress: 1%|▍ | ETA: 0:17:10 Progress: 1%|▍ | ETA: 0:17:06 Progress: 1%|▌ | ETA: 0:17:01 Progress: 1%|▌ | ETA: 0:16:59 Progress: 1%|▌ | ETA: 0:17:10 Progress: 1%|▋ | ETA: 0:17:12 Progress: 2%|▋ | ETA: 0:17:09 Progress: 2%|▋ | ETA: 0:17:08 Progress: 2%|▊ | ETA: 0:17:07 Progress: 2%|▊ | ETA: 0:17:14 Progress: 2%|▊ | ETA: 0:17:13 Progress: 2%|▉ | ETA: 0:17:11 Progress: 2%|▉ | ETA: 0:17:09 Progress: 2%|▉ | ETA: 0:17:14 Progress: 2%|█ | ETA: 0:17:12 Progress: 2%|█ | ETA: 0:17:11 Progress: 2%|█ | ETA: 0:17:09 Progress: 3%|█ | ETA: 0:17:13 Progress: 3%|█▏ | ETA: 0:17:12 Progress: 3%|█▏ | ETA: 0:17:10 Progress: 3%|█▏ | ETA: 0:17:08 Progress: 3%|█▎ | ETA: 0:17:06 Progress: 3%|█▎ | ETA: 0:17:09 Progress: 3%|█▎ | ETA: 0:17:08 Progress: 3%|█▍ | ETA: 0:17:06 Progress: 3%|█▍ | ETA: 0:17:04 Progress: 3%|█▍ | ETA: 0:17:07 Progress: 4%|█▌ | ETA: 0:17:06 Progress: 4%|█▌ | ETA: 0:17:04 Progress: 4%|█▌ | ETA: 0:17:00 Progress: 4%|█▋ | ETA: 0:16:57 Progress: 4%|█▋ | ETA: 0:16:57 Progress: 4%|█▋ | ETA: 0:16:54 Progress: 4%|█▊ | ETA: 0:16:52 Progress: 4%|█▊ | ETA: 0:16:51 Progress: 4%|█▊ | ETA: 0:16:53 Progress: 4%|█▉ | ETA: 0:16:48 Progress: 5%|█▉ | ETA: 0:16:46 Progress: 5%|█▉ | ETA: 0:16:45 Progress: 5%|██ | ETA: 0:16:46 Progress: 5%|██ | ETA: 0:16:46 Progress: 5%|██ | ETA: 0:16:44 Progress: 5%|██▏ | ETA: 0:16:43 Progress: 5%|██▏ | ETA: 0:16:41 Progress: 5%|██▏ | ETA: 0:16:43 Progress: 5%|██▎ | ETA: 0:16:42 Progress: 5%|██▎ | ETA: 0:16:41 Progress: 6%|██▎ | ETA: 0:16:40 Progress: 6%|██▎ | ETA: 0:16:38 Progress: 6%|██▍ | ETA: 0:16:40 Progress: 6%|██▍ | ETA: 0:16:39 Progress: 6%|██▍ | ETA: 0:16:37 Progress: 6%|██▌ | ETA: 0:16:36 Progress: 6%|██▌ | ETA: 0:16:36 Progress: 6%|██▌ | ETA: 0:16:34 Progress: 6%|██▋ | ETA: 0:16:31 Progress: 6%|██▋ | ETA: 0:16:30 Progress: 7%|██▋ | ETA: 0:16:28 Progress: 7%|██▊ | ETA: 0:16:28 Progress: 7%|██▊ | ETA: 0:16:25 Progress: 7%|██▊ | ETA: 0:16:22 Progress: 7%|██▉ | ETA: 0:16:22 Progress: 7%|██▉ | ETA: 0:16:24 Progress: 7%|██▉ | ETA: 0:16:22 Progress: 7%|███ | ETA: 0:16:21 Progress: 7%|███ | ETA: 0:16:20 Progress: 7%|███ | ETA: 0:16:20 Progress: 8%|███▏ | ETA: 0:16:19 Progress: 8%|███▏ | ETA: 0:16:18 Progress: 8%|███▏ | ETA: 0:16:17 Progress: 8%|███▎ | ETA: 0:16:15 Progress: 8%|███▎ | ETA: 0:16:16 Progress: 8%|███▎ | ETA: 0:16:14 Progress: 8%|███▍ | ETA: 0:16:13 Progress: 8%|███▍ | ETA: 0:16:12 Progress: 8%|███▍ | ETA: 0:16:12 Progress: 8%|███▍ | ETA: 0:16:11 Progress: 8%|███▌ | ETA: 0:16:10 Progress: 9%|███▌ | ETA: 0:16:08 Progress: 9%|███▌ | ETA: 0:16:07 Progress: 9%|███▋ | ETA: 0:16:07 Progress: 9%|███▋ | ETA: 0:16:06 Progress: 9%|███▋ | ETA: 0:16:05 Progress: 9%|███▊ | ETA: 0:16:04 Progress: 9%|███▊ | ETA: 0:16:04 Progress: 9%|███▊ | ETA: 0:16:03 Progress: 9%|███▉ | ETA: 0:16:02 Progress: 9%|███▉ | ETA: 0:16:00 Progress: 10%|███▉ | ETA: 0:15:59 Progress: 10%|████ | ETA: 0:15:59 Progress: 10%|████ | ETA: 0:15:58 Progress: 10%|████ | ETA: 0:15:57 Progress: 10%|████▏ | ETA: 0:15:55 Progress: 10%|████▏ | ETA: 0:15:56 Progress: 10%|████▏ | ETA: 0:15:54 Progress: 10%|████▎ | ETA: 0:15:53 Progress: 10%|████▎ | ETA: 0:15:52 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:57:02 Progress: 21%|████████▋ | ETA: 0:06:43 Progress: 41%|████████████████▉ | ETA: 0:02:34 Progress: 64%|██████████████████████████▎ | ETA: 0:01:02 Progress: 86%|███████████████████████████████████▎ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: 0 records are matched 231.417707 seconds (2.01 G allocations: 106.050 GiB, 8.36% gc time, 0.43% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m20.5s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:58:27 Progress: 20%|████████▏ | ETA: 0:07:17 Progress: 39%|████████████████ | ETA: 0:02:49 Progress: 63%|█████████████████████████▊ | ETA: 0:01:05 Progress: 85%|███████████████████████████████████ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: 833 records are matched 121.525439 seconds (1.01 G allocations: 53.815 GiB, 7.47% gc time, 0.53% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 16:50:30 Progress: 19%|███████▋ | ETA: 0:06:35 Progress: 38%|███████████████▊ | ETA: 0:02:26 Progress: 61%|█████████████████████████▏ | ETA: 0:00:58 Progress: 84%|██████████████████████████████████▍ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:34 [ Info: 493 records are matched 104.832505 seconds (1.01 G allocations: 53.814 GiB, 7.89% gc time, 0.60% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:49:00 Progress: 19%|███████▊ | ETA: 0:07:10 Progress: 40%|████████████████▍ | ETA: 0:02:33 Progress: 61%|█████████████████████████▏ | ETA: 0:01:05 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: 0 records are matched 114.859716 seconds (1.01 G allocations: 53.814 GiB, 7.57% gc time, 0.54% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m43.4s 1.037187 seconds (1.18 M allocations: 68.295 MiB, 2.12% gc time, 81.16% compilation time) 0.966867 seconds (1.09 M allocations: 65.112 MiB, 79.94% compilation time) 0.902606 seconds (1.09 M allocations: 64.159 MiB, 3.09% gc time, 78.81% compilation time) 0.413293 seconds (184.39 k allocations: 10.833 MiB, 99.96% compilation time) 0.010215 seconds (6.15 k allocations: 395.711 KiB, 96.53% compilation time) 0.007556 seconds (2.63 k allocations: 166.008 KiB, 95.41% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 8.7s 0.955588 seconds (963.43 k allocations: 56.638 MiB, 81.21% compilation time) 0.924349 seconds (820.64 k allocations: 50.720 MiB, 3.81% gc time, 80.45% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.0s Test Summary: | Pass Total Time convert_ds | 5 5 1.2s 0.101400 seconds (525.06 k allocations: 30.677 MiB, 29.12% compilation time) 0.611665 seconds (633.73 k allocations: 37.590 MiB, 3.41% gc time, 84.62% 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 0.084917 seconds (520.58 k allocations: 32.160 MiB, 20.48% gc time) 0.550607 seconds (584.30 k allocations: 36.202 MiB, 87.79% 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 0.145698 seconds (1.56 M allocations: 62.081 MiB, 17.69% gc time, 5.83% compilation time) 0.709775 seconds (1.68 M allocations: 70.126 MiB, 3.69% gc time, 80.43% 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 11.4s RNG of the outermost testset: Xoshiro(0x18148fed5a6a802f, 0x15f4282e9af2796b, 0x5097e16dd5a14971, 0x402253c26baf3546, 0xadd8b9ef4932d08f) 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 1131.04s 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] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:355 [12] _start() @ Base ./client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1566.16s: package has test failures