Package evaluation to test VCFTools on Julia 1.14.0-DEV.1640 (5532bea546*) started at 2026-01-30T11:44:22.110 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.64s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed DelimitedFiles ────────── v1.9.1 Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed MacroTools ────────────── v0.5.16 Installed CommonSolve ───────────── v0.2.6 Installed DataStructures ────────── v0.19.3 Installed FillArrays ────────────── v1.16.0 Installed ConstructionBase ──────── v1.6.0 Installed VCFTools ──────────────── v0.2.10 Installed CodecZlib ─────────────── v0.7.8 Installed StatsBase ─────────────── v0.34.10 Installed OrderedCollections ────── v1.8.1 Installed HypothesisTests ───────── v0.11.6 Installed TranscodingStreams ────── v0.11.3 Installed HypergeometricFunctions ─ v0.3.28 Installed Combinatorics ─────────── v1.1.0 Installed AliasTables ───────────── v1.1.3 Installed StatsAPI ──────────────── v1.8.0 Installed IrrationalConstants ───── v0.2.6 Installed ProgressMeter ─────────── v1.11.0 Installed Statistics ────────────── v1.11.1 Installed SIMD ──────────────────── v3.7.2 Installed PrecompileTools ───────── v1.3.3 Installed DataAPI ───────────────── v1.16.0 Installed QuadGK ────────────────── v2.11.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed LogExpFunctions ───────── v0.3.29 Installed Rmath ─────────────────── v0.9.0 Installed BufferedStreams ───────── v1.2.2 Installed PtrArrays ─────────────── v1.3.0 Installed BioGenerics ───────────── v0.1.5 Installed StatsFuns ─────────────── v1.5.2 Installed Roots ─────────────────── v2.2.10 Installed Distributions ─────────── v0.25.123 Installed Preferences ───────────── v1.5.1 Installed JLLWrappers ───────────── v1.7.1 Installed Automa ────────────────── v1.1.0 Installed Reexport ──────────────── v1.2.2 Installed InverseFunctions ──────── v0.1.17 Installed Missings ──────────────── v1.2.0 Installed SpecialFunctions ──────── v2.6.1 Installed PDMats ────────────────── v0.11.37 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.9 Installed Accessors ─────────────── v0.1.43 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 8.74s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5014.7 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4733.2 ms ✓ MacroTools 1730.1 ms ✓ InlineStrings 838.8 ms ✓ Reexport 1193.7 ms ✓ Statistics 954.7 ms ✓ DataAPI 1210.1 ms ✓ ConstructionBase 2186.5 ms ✓ IrrationalConstants 829.1 ms ✓ DataValueInterfaces 944.0 ms ✓ StatsAPI 1335.4 ms ✓ OrderedCollections 894.7 ms ✓ InvertedIndices 995.3 ms ✓ InverseFunctions 920.8 ms ✓ CompositionsBase 1210.3 ms ✓ DocStringExtensions 2300.3 ms ✓ Combinatorics 1062.5 ms ✓ WorkerUtilities 2224.2 ms ✓ FillArrays 1090.7 ms ✓ BufferedStreams 888.7 ms ✓ PtrArrays 863.0 ms ✓ CommonSolve 1364.6 ms ✓ TranscodingStreams 855.3 ms ✓ IteratorInterfaceExtensions 906.3 ms ✓ LaTeXStrings 1945.3 ms ✓ Crayons 1882.6 ms ✓ PDMats 1053.9 ms ✓ DelimitedFiles 1889.5 ms ✓ ProgressMeter 2177.7 ms ✓ SentinelArrays 1214.1 ms ✓ Compat 1223.0 ms ✓ Preferences 1389.4 ms ✓ Statistics → SparseArraysExt 1233.2 ms ✓ Missings 1317.2 ms ✓ PooledArrays 1008.4 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3720.6 ms ✓ DataStructures 1762.6 ms ✓ InverseFunctions → InverseFunctionsTestExt 932.9 ms ✓ InverseFunctions → InverseFunctionsDatesExt 943.2 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1447.4 ms ✓ LogExpFunctions 1555.9 ms ✓ FillArrays → FillArraysSparseArraysExt 1035.1 ms ✓ FillArrays → FillArraysStatisticsExt 1037.3 ms ✓ AliasTables 1030.7 ms ✓ BioGenerics 1019.8 ms ✓ CodecZlib 840.8 ms ✓ TableTraits 1515.1 ms ✓ FillArrays → FillArraysPDMatsExt 923.0 ms ✓ Compat → CompatLinearAlgebraExt 1293.2 ms ✓ JLLWrappers 1023.5 ms ✓ PrecompileTools 1159.8 ms ✓ SortingAlgorithms 2386.0 ms ✓ QuadGK 5348.8 ms ✓ Accessors 859.6 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1069.1 ms ✓ BGZFStreams 1809.7 ms ✓ Tables 2170.5 ms ✓ FilePathsBase 1465.2 ms ✓ Rmath_jll 1497.7 ms ✓ OpenSpecFun_jll 3240.6 ms ✓ StringManipulation 14784.4 ms ✓ SIMD 17362.2 ms ✓ Parsers 4649.5 ms ✓ StatsBase 2427.9 ms ✓ Accessors → LinearAlgebraExt 1929.4 ms ✓ Accessors → TestExt 2967.4 ms ✓ FilePathsBase → FilePathsBaseTestExt 1038.9 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1616.1 ms ✓ Rmath 5113.1 ms ✓ SpecialFunctions 41615.7 ms ✓ PrettyTables 19483.4 ms ✓ Automa 1330.2 ms ✓ InlineStrings → ParsersExt 2033.4 ms ✓ PDMats → StatsBaseExt 7786.0 ms ✓ Roots 2371.4 ms ✓ HypergeometricFunctions 88495.2 ms ✓ DataFrames [ Info: Compiling VCF parser... 15799.9 ms ✓ VariantCallFormat 2495.5 ms ✓ WeakRefStrings 2925.1 ms ✓ StatsFuns 26556.5 ms ✓ CSV 1013.1 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9328.4 ms ✓ Distributions 3656.3 ms ✓ Distributions → DistributionsTestExt 4347.2 ms ✓ HypothesisTests 4465.5 ms ✓ VCFTools 84 dependencies successfully precompiled in 375 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 399.53s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_uy7ln9/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.10 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_uy7ln9/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.6 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.18.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.5s Test Summary: | Pass Total Time openvcf | 4 4 3.1s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.3s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.3s ┌ 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: 0:32:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 13.721466 seconds (8.95 M allocations: 542.009 MiB, 5.35% gc time, 92.23% compilation time: 16% of which was recompilation) 0.448938 seconds (2.37 M allocations: 141.172 MiB, 20.77% gc time, 13.01% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:30:31 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.234840 seconds (3.89 M allocations: 235.981 MiB, 1.14% gc time, 83.57% compilation time) 0.423440 seconds (2.37 M allocations: 141.301 MiB, 4.94% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.3s 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 1.7s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.5s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:51 Progress: 0%|▏ | ETA: 0:17:22 Progress: 0%|▏ | ETA: 0:20:20 Progress: 0%|▏ | ETA: 0:19:22 Progress: 0%|▎ | ETA: 0:18:50 Progress: 1%|▎ | ETA: 0:18:19 Progress: 1%|▎ | ETA: 0:19:10 Progress: 1%|▍ | ETA: 0:18:59 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100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:42:08 Progress: 20%|████████▏ | ETA: 0:07:33 Progress: 39%|████████████████ | ETA: 0:02:56 Progress: 57%|███████████████████████▎ | ETA: 0:01:27 Progress: 77%|███████████████████████████████▌ | ETA: 0:00:35 Progress: 99%|████████████████████████████████████████▋| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 823 records are matched 238.172720 seconds (2.01 G allocations: 106.138 GiB, 12.92% gc time, 0.54% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:16:32 Progress: 0%|▏ | ETA: 0:16:22 Progress: 0%|▏ | ETA: 0:16:29 Progress: 0%|▏ | ETA: 0:18:33 Progress: 1%|▎ | ETA: 0:18:14 Progress: 1%|▎ | ETA: 0:17:50 Progress: 1%|▎ | ETA: 0:17:35 Progress: 1%|▍ | ETA: 0:17:23 Progress: 1%|▍ | ETA: 0:18:07 Progress: 1%|▍ | ETA: 0:18:09 Progress: 1%|▌ | ETA: 0:17:58 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Progress: 57%|███████████████████████▌ | ETA: 0:01:23 Progress: 78%|████████████████████████████████▏ | ETA: 0:00:31 Progress: 99%|████████████████████████████████████████▋| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: 488 records are matched 232.892730 seconds (2.01 G allocations: 106.120 GiB, 13.25% gc time, 0.38% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:12:23 Progress: 0%|▏ | ETA: 0:13:25 Progress: 0%|▏ | ETA: 0:13:27 Progress: 1%|▎ | ETA: 0:15:47 Progress: 1%|▎ | ETA: 0:15:58 Progress: 1%|▎ | ETA: 0:16:07 Progress: 1%|▍ | ETA: 0:16:04 Progress: 1%|▍ | ETA: 0:16:01 Progress: 1%|▍ | ETA: 0:16:58 Progress: 1%|▌ | ETA: 0:17:05 Progress: 1%|▌ | ETA: 0:17:00 Progress: 1%|▌ | ETA: 0:16:52 Progress: 1%|▋ | ETA: 0:16:47 Progress: 2%|▋ | ETA: 0:16:48 Progress: 2%|▋ | ETA: 0:17:21 Progress: 2%|▊ | ETA: 0:17:22 Progress: 2%|▊ | ETA: 0:17:18 Progress: 2%|▊ | ETA: 0:17:14 Progress: 2%|▉ | ETA: 0:17:08 Progress: 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| ETA: 0:16:51 Progress: 8%|███▌ | ETA: 0:16:49 Progress: 9%|███▌ | ETA: 0:16:48 Progress: 9%|███▌ | ETA: 0:16:46 Progress: 9%|███▋ | ETA: 0:16:51 Progress: 9%|███▋ | ETA: 0:16:49 Progress: 9%|███▋ | ETA: 0:16:47 Progress: 9%|███▊ | ETA: 0:16:45 Progress: 9%|███▊ | ETA: 0:16:43 Progress: 9%|███▊ | ETA: 0:16:41 Progress: 9%|███▉ | ETA: 0:16:45 Progress: 9%|███▉ | ETA: 0:16:44 Progress: 10%|███▉ | ETA: 0:16:42 Progress: 10%|████ | ETA: 0:16:40 Progress: 10%|████ | ETA: 0:16:38 Progress: 10%|████ | ETA: 0:16:37 Progress: 10%|████▏ | ETA: 0:16:39 Progress: 10%|████▏ | ETA: 0:16:37 Progress: 10%|████▏ | ETA: 0:16:34 Progress: 10%|████▎ | ETA: 0:16:31 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:07:13 Progress: 19%|████████ | ETA: 0:07:27 Progress: 39%|███████████████▉ | ETA: 0:02:53 Progress: 55%|██████████████████████▊ | ETA: 0:01:29 Progress: 73%|█████████████████████████████▊ | ETA: 0:00:42 Progress: 96%|███████████████████████████████████████▎ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 0 records are matched 236.886809 seconds (2.01 G allocations: 106.120 GiB, 13.53% gc time, 0.36% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m55.3s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:28:37 Progress: 19%|███████▊ | ETA: 0:08:17 Progress: 37%|███████████████▎ | ETA: 0:03:16 Progress: 55%|██████████████████████▊ | ETA: 0:01:35 Progress: 77%|███████████████████████████████▋ | ETA: 0:00:35 Progress: 99%|████████████████████████████████████████▍| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:02:00 [ Info: 833 records are matched 130.508743 seconds (1.02 G allocations: 53.885 GiB, 12.47% gc time, 0.46% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:19:28 Progress: 17%|███████ | ETA: 0:09:20 Progress: 38%|███████████████▌ | ETA: 0:03:10 Progress: 60%|████████████████████████▊ | ETA: 0:01:17 Progress: 81%|█████████████████████████████████▎ | ETA: 0:00:27 Progress: 100%|█████████████████████████████████████████| Time: 0:01:58 [ Info: 493 records are matched 128.940325 seconds (1.02 G allocations: 53.884 GiB, 12.28% gc time, 0.49% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:27:36 Progress: 17%|██████▉ | ETA: 0:09:09 Progress: 36%|██████████████▋ | ETA: 0:03:20 Progress: 59%|████████████████████████ | ETA: 0:01:19 Progress: 81%|█████████████████████████████████▍ | ETA: 0:00:26 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: 0 records are matched 124.628945 seconds (1.02 G allocations: 53.884 GiB, 12.26% gc time, 0.45% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m26.6s 1.109747 seconds (1.14 M allocations: 65.233 MiB, 2.31% gc time, 80.85% compilation time) 0.922132 seconds (1.05 M allocations: 62.200 MiB, 81.95% compilation time) 0.984027 seconds (1.05 M allocations: 61.241 MiB, 3.14% gc time, 81.74% compilation time) 0.413824 seconds (174.71 k allocations: 10.089 MiB, 99.96% compilation time) 0.010437 seconds (6.05 k allocations: 389.102 KiB, 96.13% compilation time) 0.009617 seconds (2.62 k allocations: 164.711 KiB, 96.53% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.1s 0.867267 seconds (950.47 k allocations: 56.084 MiB, 80.17% compilation time) 0.882578 seconds (812.56 k allocations: 50.415 MiB, 3.48% gc time, 76.68% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.4s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.105078 seconds (525.04 k allocations: 30.674 MiB, 30.77% compilation time) 0.679318 seconds (624.15 k allocations: 36.947 MiB, 3.40% gc time, 85.04% 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 0.084100 seconds (520.58 k allocations: 32.160 MiB, 22.23% gc time) 0.543351 seconds (582.87 k allocations: 36.186 MiB, 87.56% 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 0.185712 seconds (1.56 M allocations: 62.079 MiB, 32.91% gc time, 4.31% compilation time) 1.079633 seconds (1.68 M allocations: 69.745 MiB, 45.12% gc time, 43.68% 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 Total Time convert to transpose functions | 13 13 7.2s Test Summary: | Pass Total Time record info | 14 14 4.8s Test Summary: | Pass Total Time write VCF | 3 3 4.1s 2.129694 seconds (4.73 M allocations: 295.158 MiB, 3.02% gc time, 54.85% compilation time) 1.097723 seconds (2.39 M allocations: 142.476 MiB, 8.17% gc time, 20.78% compilation time) 0.963207 seconds (4.42 M allocations: 276.458 MiB, 5.14% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.0s 0.979885 seconds (591.13 k allocations: 33.116 MiB, 2.29% gc time, 42.01% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.8s Test Summary: | Pass Total Time filter_chr | 4 4 1.6s Progress: 0%|▏ | ETA: 0:20:25 Progress: 1%|▍ | ETA: 0:21:15 Progress: 1%|▌ | ETA: 0:20:45 Progress: 2%|▋ | ETA: 0:20:16 Progress: 2%|▉ | ETA: 0:20:01 Progress: 3%|█ | ETA: 0:19:52 Progress: 3%|█▎ | ETA: 0:19:49 Progress: 3%|█▍ | ETA: 0:19:51 Progress: 4%|█▌ | ETA: 0:19:48 Progress: 4%|█▊ | ETA: 0:19:36 Progress: 5%|█▉ | ETA: 0:19:21 Progress: 5%|██▏ | ETA: 0:19:09 Progress: 5%|██▎ | ETA: 0:18:56 Progress: 6%|██▍ | ETA: 0:18:49 Progress: 6%|██▋ | ETA: 0:18:59 Progress: 7%|██▊ | ETA: 0:18:54 Progress: 7%|███ | ETA: 0:18:50 Progress: 8%|███▏ | ETA: 0:18:56 Progress: 8%|███▎ | ETA: 0:18:51 Progress: 8%|███▌ | ETA: 0:18:51 Progress: 9%|███▋ | ETA: 0:18:29 Progress: 9%|███▉ | ETA: 0:18:26 Progress: 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A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 343 running 1 of 1 signal (10): User defined signal 1 immut_id_ at /source/src/builtins.c:450 ijl_object_id_ at /source/src/builtins.c:510 [inlined] jl_table_peek_bp at /source/src/iddict.c:118 [inlined] ijl_eqtable_get at /source/src/iddict.c:157 get at ./iddict.jl:92 [inlined] in at ./iddict.jl:182 [inlined] haskey at ./abstractdict.jl:19 [inlined] deepcopy_internal at ./deepcopy.jl:138 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x70419fdb55d6) at (unknown file) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 _deepcopy_memory_t at ./deepcopy.jl:120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x70418e5f1a76) at (unknown file) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_invoke at /source/src/gf.c:4127 ijl_eval_thunk at /source/src/toplevel.c:757 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x70419fd005d2) at (unknown file) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:765 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_74896.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:765 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_50962.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7041b5f2a249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Progress: 83%|██████████████████████████████████▏ | ETA: 0:03:20 ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Progress: 84%|██████████████████████████████████▍ | ETA: 0:03:13┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000070419b9fc010 Total snapshots: 614. Utilization: 100% ╎614 @Base/client.jl:585 _start() ╎ 614 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 614 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 614 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 614 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 614 @Base/loading.jl:3211 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 614 @Base/loading.jl:3151 include_string(mapexpr::typeof(identity), m… ╎ ╎ 614 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 614 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 614 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 614 @Base/loading.jl:3211 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 614 @Base/loading.jl:3151 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 614 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 614 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 614 @Test/src/Test.jl:2244 macro expansion ╎ ╎ ╎ 614 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 614 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 3╎ ╎ ╎ ╎ 98 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 12 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 12 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 5 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1003 getindex ╎ ╎ ╎ ╎ ╎ 3 @Base/…ators.jl:424 > 3╎ ╎ ╎ ╎ ╎ 3 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 1 @VCFTools/…t.jl:225 geno_ismissing 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1002 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1003 getindex ╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1002 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:381 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1003 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:134 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:3197 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:943 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 73 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 71 @Base/array.jl:2500 findfirst 1╎ ╎ ╎ ╎ 69 @Base/array.jl:2449 findnext 7╎ ╎ ╎ ╎ ╎ 7 @Base/…tials.jl:1003 getindex ╎ ╎ ╎ ╎ ╎ 61 @Base/…ators.jl:1203 Fix ╎ ╎ ╎ ╎ ╎ 61 @Base/…tors.jl:1203 #_#59 ╎ ╎ ╎ ╎ ╎ 61 @Base/…tors.jl:178 isequal 61╎ ╎ ╎ ╎ ╎ 61 @Base/…ring.jl:187 == ╎ ╎ ╎ ╎ 2 @Base/array.jl:2450 findnext 2╎ ╎ ╎ ╎ ╎ 2 @Base/…otion.jl:637 == 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:1003 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 1 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2449 findnext ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:673 isequaldata 1╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:677 memcmp 1╎ ╎ ╎ ╎ 4 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1003 getindex ╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:225 geno_ismissing ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1002 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:385 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1003 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:82 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3197 getindex ╎ ╎ ╎ ╎ 1 @Base/range.jl:955 _getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:83 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:1002 getindex ╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:385 checkbounds 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:381 checkbounds ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:86 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1003 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:99 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:261 log(x::Float64) ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:289 _log ╎ ╎ ╎ ╎ ╎ 1 @Base/…l/log.jl:163 log_proc1 1╎ ╎ ╎ ╎ ╎ 1 @Base/float.jl:492 + ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:45 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:483 next! ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:484 #next!#15 ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:465 lock_if_threading 1╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:453 is_threading ╎ ╎ ╎ ╎ 515 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 515 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 121 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 121 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 121 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2125 empty! 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1289 _deleteend! ╎ ╎ ╎ ╎ ╎ 97 @VariantCallFormat/…:165 _read!(reader::VariantCa… 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 macro expansion ╎ ╎ ╎ ╎ ╎ 95 @Automa/…en.jl:449 macro expansion 1╎ ╎ ╎ ╎ ╎ 1 @Base/…iler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ 60 @Base/array.jl:436 getindex 59╎ ╎ ╎ ╎ ╎ 60 @Base/boot.jl:676 Array ╎ ╎ ╎ ╎ ╎ 32 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 30 @Base/…ray.jl:1348 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1197 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1204 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 1╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ray.jl:1205 _growend! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1158 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1159 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1169 _growend_internal!(a::Vect… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:341 div ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1180 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1096 overallocation ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1097 overallocation 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:341 div ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ay.jl:1101 array_new_memory 14╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ot.jl:615 GenericMemory 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1189 _growend_internal!(a::Vect… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:1190 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1349 _push! 1╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1044 __safe_setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:1003 getindex ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…dvec.jl:491 all ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…dvec.jl:486 reduce ╎ ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…ics.jl:1050 reduce_and 1╎ ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…cs.jl:1065 macro expansion ╎ ╎ ╎ ╎ ╎ 23 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 23 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 23 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 23 @BufferedStreams/…:5 readbytes! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:0 readbytes!(s::TranscodingStream… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/io.jl:1167 readbytes!(s::TranscodingStr… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:209 eof ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:195 process(codec::GzipDec… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 15 @Base/io.jl:1168 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 14 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:298 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:208 eof 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ ╎ 12 @TranscodingStreams/…:302 peek 12╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ls.jl:1003 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:307 read ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:97 consumed! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:98 #consumed!#1 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/io.jl:1174 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:393 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1020 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1024 _setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1025 _setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ 394 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 394 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:384 copy 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:615 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:385 copy ╎ ╎ ╎ ╎ ╎ 1 @Base/…emory.jl:139 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ 1 @Base/cmem.jl:28 memmove ╎ ╎ ╎ ╎ ╎ 392 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 392 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 392 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 1╎ ╎ ╎ ╎ ╎ 392 @Base/…copy.jl:104 deepcopy_internal ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:615 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:621 memoryref 28╎ ╎ ╎ ╎ ╎ 28 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 10╎ ╎ ╎ ╎ ╎ 10 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 10╎ ╎ ╎ ╎ ╎ 10 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 26╎ ╎ ╎ ╎ ╎ 307 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ct.jl:182 in 33╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 39 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:688 Array 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ot.jl:676 Array ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ict.jl:81 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:88 * ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:580 >> 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:573 >> 33╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ict.jl:86 setindex! 8╎ ╎ ╎ ╎ ╎ ╎ 209 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… ╎ ╎ ╎ ╎ ╎ ╎ 84 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 84 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 84 @Base/…ct.jl:182 in 81╎ ╎ ╎ ╎ ╎ ╎ 84 @Base/…ct.jl:92 get 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 115 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…ct.jl:182 in 31╎ ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…ct.jl:92 get 5╎ ╎ ╎ ╎ ╎ ╎ 84 @Base/…py.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 15╎ ╎ ╎ ╎ ╎ ╎ 75 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:189 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ry.jl:193 copy(a::Memory{UnitRange… 13╎ ╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…ot.jl:615 GenericMemory 2╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:194 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ry.jl:157 unsafe_copyto! 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ot.jl:622 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ry.jl:139 unsafe_copyto! 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…em.jl:28 memmove 34╎ ╎ ╎ ╎ ╎ ╎ 34 @Base/…ct.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:0 _deepcopy_memory_t(x::Memor… 25╎ ╎ ╎ ╎ ╎ 25 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 8╎ ╎ ╎ ╎ ╎ 8 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:125 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:925 iterate 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ion.jl:637 == ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1246 wait_forever at ./task.jl:1168 jfptr_wait_forever_46727.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000745111b0bee0 Total snapshots: 365. Utilization: 0% ╎365 @Base/task.jl:1168 wait_forever() 364╎ 365 @Base/task.jl:1246 wait() Progress: 84%|██████████████████████████████████▋ | ETA: 0:03:08 [343] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 jl_f_memoryrefget at /source/src/builtins.c:1881 _deepcopy_memory_t at ./deepcopy.jl:118 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x70418e5f1a76) at (unknown file) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.14/Test/src/Test.jl:2244 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_invoke at /source/src/gf.c:4127 ijl_eval_thunk at /source/src/toplevel.c:757 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x70419fd005d2) at (unknown file) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:765 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_74896.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:765 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:779 ijl_toplevel_eval_in at /source/src/toplevel.c:824 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_50962.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4120 [inlined] ijl_apply_generic at /source/src/gf.c:4317 jl_apply at /source/src/julia.h:2285 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7041b5f2a249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 17363653365 (Pool: 17363637890; Big: 15475); GC: 17657 PkgEval terminated after 2726.48s: test duration exceeded the time limit