Package evaluation to test VCFTools on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-25T18:48:35.122 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.71s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed DelimitedFiles ────────── v1.9.1 Installed MacroTools ────────────── v0.5.16 Installed DataStructures ────────── v0.19.3 Installed FillArrays ────────────── v1.15.0 Installed CommonSolve ───────────── v0.2.4 Installed ConstructionBase ──────── v1.6.0 Installed HypergeometricFunctions ─ v0.3.28 Installed VCFTools ──────────────── v0.2.10 Installed AliasTables ───────────── v1.1.3 Installed CodecZlib ─────────────── v0.7.8 Installed OrderedCollections ────── v1.8.1 Installed TranscodingStreams ────── v0.11.3 Installed StatsBase ─────────────── v0.34.8 Installed SIMD ──────────────────── v3.7.2 Installed StatsAPI ──────────────── v1.7.1 Installed DataAPI ───────────────── v1.16.0 Installed Combinatorics ─────────── v1.0.3 Installed ProgressMeter ─────────── v1.11.0 Installed Statistics ────────────── v1.11.1 Installed PrecompileTools ───────── v1.3.3 Installed HypothesisTests ───────── v0.11.6 Installed IrrationalConstants ───── v0.2.6 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Rmath ─────────────────── v0.9.0 Installed LogExpFunctions ───────── v0.3.29 Installed BufferedStreams ───────── v1.2.2 Installed QuadGK ────────────────── v2.11.2 Installed Roots ─────────────────── v2.2.10 Installed Distributions ─────────── v0.25.122 Installed StatsFuns ─────────────── v1.5.2 Installed PtrArrays ─────────────── v1.3.0 Installed Reexport ──────────────── v1.2.2 Installed Missings ──────────────── v1.2.0 Installed InverseFunctions ──────── v0.1.17 Installed SpecialFunctions ──────── v2.6.1 Installed Preferences ───────────── v1.5.0 Installed BioGenerics ───────────── v0.1.5 Installed JLLWrappers ───────────── v1.7.1 Installed Automa ────────────────── v1.1.0 Installed PDMats ────────────────── v0.11.36 Installed Accessors ─────────────── v0.1.42 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.9 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 v0.1.42 [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 v1.0.3 [38540f10] + CommonSolve v0.2.4 [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 v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [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 v0.11.36 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [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 v1.7.1 [2913bbd2] + StatsBase v0.34.8 [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 v0.3.29+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 8.16s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4673.8 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4225.4 ms ✓ MacroTools 766.5 ms ✓ Reexport 1075.0 ms ✓ Statistics 847.4 ms ✓ DataAPI 1114.4 ms ✓ ConstructionBase 2083.7 ms ✓ IrrationalConstants 798.6 ms ✓ StatsAPI 1240.5 ms ✓ OrderedCollections 897.5 ms ✓ InverseFunctions 787.3 ms ✓ CompositionsBase 1091.1 ms ✓ DocStringExtensions 2112.9 ms ✓ Combinatorics 2097.6 ms ✓ FillArrays 1014.3 ms ✓ BufferedStreams 784.4 ms ✓ PtrArrays 742.9 ms ✓ CommonSolve 1239.4 ms ✓ TranscodingStreams 1231.5 ms ✓ SuiteSparse 947.4 ms ✓ DelimitedFiles 1764.6 ms ✓ ProgressMeter 1108.6 ms ✓ Preferences 1301.8 ms ✓ Statistics → SparseArraysExt 946.9 ms ✓ Missings 736.5 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 3230.7 ms ✓ DataStructures 734.5 ms ✓ InverseFunctions → InverseFunctionsDatesExt 697.6 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1129.7 ms ✓ LogExpFunctions 1240.4 ms ✓ FillArrays → FillArraysSparseArraysExt 786.0 ms ✓ FillArrays → FillArraysStatisticsExt 806.6 ms ✓ AliasTables 771.3 ms ✓ BioGenerics 835.3 ms ✓ CodecZlib 1551.1 ms ✓ PDMats 991.6 ms ✓ JLLWrappers 744.0 ms ✓ PrecompileTools 876.3 ms ✓ SortingAlgorithms 1896.3 ms ✓ QuadGK 3941.3 ms ✓ Accessors 674.9 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 814.1 ms ✓ BGZFStreams 1168.3 ms ✓ FillArrays → FillArraysPDMatsExt 1134.3 ms ✓ Rmath_jll 1133.7 ms ✓ OpenSpecFun_jll 13469.2 ms ✓ SIMD 3884.9 ms ✓ StatsBase 2315.4 ms ✓ Accessors → LinearAlgebraExt 1316.7 ms ✓ Rmath 4220.7 ms ✓ SpecialFunctions 17117.7 ms ✓ Automa 1166.6 ms ✓ PDMats → StatsBaseExt 5423.2 ms ✓ Roots 1950.7 ms ✓ HypergeometricFunctions [ Info: Compiling VCF parser... 15434.6 ms ✓ VariantCallFormat 2335.1 ms ✓ StatsFuns 831.3 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 7524.4 ms ✓ Distributions 3421.3 ms ✓ HypothesisTests 5620.9 ms ✓ VCFTools 59 dependencies successfully precompiled in 142 seconds. 11 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 158.82s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_PaIHAi/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.8 [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_PaIHAi/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [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 v1.0.3 [38540f10] CommonSolve v0.2.4 [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 v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [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 v0.11.36 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [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 v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.8 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL 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 v8.17.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+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 8.8s Test Summary: | Pass Total Time openvcf | 4 4 2.9s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.6s ┌ 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: 0:32:52 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 14.357921 seconds (10.04 M allocations: 564.179 MiB, 4.40% gc time, 96.09% compilation time: 18% of which was recompilation) 0.408555 seconds (2.40 M allocations: 144.089 MiB, 13.59% gc time, 16.28% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:29:20 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.095404 seconds (4.03 M allocations: 238.205 MiB, 2.41% gc time, 85.23% compilation time) 0.426034 seconds (2.38 M allocations: 143.160 MiB, 6.47% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.7s 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 2.2s 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 5.9s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:38 Progress: 0%|▏ | ETA: 0:17:45 Progress: 0%|▏ | ETA: 0:17:32 Progress: 0%|▏ | ETA: 0:17:23 Progress: 0%|▎ | ETA: 0:17:00 Progress: 1%|▎ | ETA: 0:16:57 Progress: 1%|▎ | ETA: 0:16:46 Progress: 1%|▍ | ETA: 0:16:45 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IDs Progress: 0%| | ETA: 17:11:16 Progress: 20%|████████ | ETA: 0:06:20 Progress: 39%|████████████████ | ETA: 0:02:25 Progress: 60%|████████████████████████▌ | ETA: 0:01:03 Progress: 81%|█████████████████████████████████▏ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:36 [ Info: 823 records are matched 207.839091 seconds (2.01 G allocations: 106.139 GiB, 7.11% gc time, 0.61% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:49 Progress: 0%|▏ | ETA: 0:17:36 Progress: 0%|▏ | ETA: 0:17:36 Progress: 0%|▏ | ETA: 0:17:31 Progress: 0%|▎ | ETA: 0:17:28 Progress: 1%|▎ | ETA: 0:17:23 Progress: 1%|▎ | ETA: 0:17:16 Progress: 1%|▍ | ETA: 0:17:10 Progress: 1%|▍ | ETA: 0:17:11 Progress: 1%|▍ | ETA: 0:17:11 Progress: 1%|▍ | ETA: 0:17:09 Progress: 1%|▌ | ETA: 0:17:05 Progress: 1%|▌ | ETA: 0:17:02 Progress: 1%|▌ | ETA: 0:16:59 Progress: 1%|▋ | ETA: 0:16:57 Progress: 2%|▋ | ETA: 0:16:55 Progress: 2%|▋ | ETA: 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Progress: 61%|█████████████████████████▏ | ETA: 0:01:05 Progress: 83%|██████████████████████████████████ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 488 records are matched 220.865937 seconds (2.01 G allocations: 106.121 GiB, 6.78% gc time, 0.38% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:13 Progress: 0%|▏ | ETA: 0:18:23 Progress: 0%|▏ | ETA: 0:18:00 Progress: 0%|▏ | ETA: 0:17:43 Progress: 0%|▎ | ETA: 0:17:33 Progress: 1%|▎ | ETA: 0:16:47 Progress: 1%|▎ | ETA: 0:16:40 Progress: 1%|▍ | ETA: 0:16:33 Progress: 1%|▍ | ETA: 0:16:30 Progress: 1%|▍ | ETA: 0:16:30 Progress: 1%|▌ | ETA: 0:16:27 Progress: 1%|▌ | ETA: 0:16:26 Progress: 1%|▌ | ETA: 0:16:27 Progress: 1%|▋ | ETA: 0:16:29 Progress: 2%|▋ | ETA: 0:16:29 Progress: 2%|▋ | ETA: 0:16:28 Progress: 2%|▊ | ETA: 0:16:30 Progress: 2%|▊ | ETA: 0:16:31 Progress: 2%|▊ | ETA: 0:16:32 Progress: 2%|▉ | ETA: 0:16:32 Progress: 2%|▉ | ETA: 0:16:32 Progress: 2%|▉ | 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ETA: 0:15:28 Progress: 9%|███▌ | ETA: 0:15:27 Progress: 9%|███▋ | ETA: 0:15:26 Progress: 9%|███▋ | ETA: 0:15:25 Progress: 9%|███▋ | ETA: 0:15:24 Progress: 9%|███▊ | ETA: 0:15:23 Progress: 9%|███▊ | ETA: 0:15:22 Progress: 9%|███▊ | ETA: 0:15:21 Progress: 9%|███▉ | ETA: 0:15:20 Progress: 9%|███▉ | ETA: 0:15:19 Progress: 9%|███▉ | ETA: 0:15:18 Progress: 10%|███▉ | ETA: 0:15:17 Progress: 10%|████ | ETA: 0:15:16 Progress: 10%|████ | ETA: 0:15:15 Progress: 10%|████ | ETA: 0:15:15 Progress: 10%|████▏ | ETA: 0:15:14 Progress: 10%|████▏ | ETA: 0:15:13 Progress: 10%|████▏ | ETA: 0:15:12 Progress: 10%|████▎ | ETA: 0:15:11 Progress: 100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:14:32 Progress: 21%|████████▌ | ETA: 0:06:34 Progress: 42%|█████████████████▎ | ETA: 0:02:24 Progress: 63%|██████████████████████████ | ETA: 0:01:01 Progress: 86%|███████████████████████████████████▏ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 0 records are matched 222.353426 seconds (2.01 G allocations: 106.120 GiB, 6.75% gc time, 0.38% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 10m58.8s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:35:49 Progress: 19%|████████ | ETA: 0:06:55 Progress: 39%|████████████████▏ | ETA: 0:02:36 Progress: 61%|█████████████████████████▏ | ETA: 0:01:05 Progress: 84%|██████████████████████████████████▎ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: 833 records are matched 114.114954 seconds (1.02 G allocations: 53.885 GiB, 6.72% gc time, 0.52% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:13:29 Progress: 20%|████████▏ | ETA: 0:06:55 Progress: 40%|████████████████▋ | ETA: 0:02:34 Progress: 63%|█████████████████████████▊ | ETA: 0:01:02 Progress: 85%|███████████████████████████████████ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 493 records are matched 117.256997 seconds (1.02 G allocations: 53.885 GiB, 6.58% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 18:58:17 Progress: 21%|████████▊ | ETA: 0:06:16 Progress: 43%|█████████████████▊ | ETA: 0:02:14 Progress: 66%|██████████████████████████▉ | ETA: 0:00:54 Progress: 90%|████████████████████████████████████▉ | ETA: 0:00:12 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 0 records are matched 115.449287 seconds (1.02 G allocations: 53.885 GiB, 6.72% gc time, 0.52% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m49.0s 1.135807 seconds (1.27 M allocations: 68.061 MiB, 5.06% gc time, 83.48% compilation time) 0.934788 seconds (1.15 M allocations: 64.043 MiB, 79.21% compilation time) 0.934562 seconds (1.15 M allocations: 63.088 MiB, 4.23% gc time, 76.96% compilation time) 0.397785 seconds (205.71 k allocations: 10.695 MiB, 99.95% compilation time) 0.009687 seconds (6.49 k allocations: 394.961 KiB, 96.25% compilation time) 0.008188 seconds (2.65 k allocations: 165.383 KiB, 95.70% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 8.8s 0.892911 seconds (977.49 k allocations: 54.491 MiB, 80.04% compilation time) 0.905767 seconds (878.92 k allocations: 51.576 MiB, 11.26% gc time, 69.12% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.6s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.126304 seconds (525.76 k allocations: 30.690 MiB, 24.05% compilation time) 0.613924 seconds (645.57 k allocations: 37.293 MiB, 84.17% 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 0.075872 seconds (520.58 k allocations: 32.160 MiB) 0.568527 seconds (595.93 k allocations: 36.387 MiB, 5.38% gc time, 79.64% 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 0.156291 seconds (1.56 M allocations: 62.080 MiB, 17.78% gc time, 5.08% compilation time) 0.559002 seconds (1.71 M allocations: 70.258 MiB, 79.70% 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 6.3s Test Summary: | Pass Total Time record info | 14 14 5.0s Test Summary: | Pass Total Time write VCF | 3 3 4.1s 1.992139 seconds (4.80 M allocations: 296.643 MiB, 4.25% gc time, 54.28% compilation time) 1.003804 seconds (2.39 M allocations: 142.700 MiB, 3.52% gc time, 22.41% compilation time) 0.932070 seconds (4.42 M allocations: 276.335 MiB, 8.05% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.7s 0.957565 seconds (605.36 k allocations: 33.376 MiB, 45.81% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.7s Test Summary: | Pass Total Time filter_chr | 4 4 1.8s Progress: 0%|▏ | ETA: 0:20:15 Progress: 1%|▍ | ETA: 0:19:54 Progress: 1%|▌ | ETA: 0:19:30 Progress: 2%|▊ | ETA: 0:19:14 Progress: 2%|▉ | ETA: 0:19:02 Progress: 3%|█ | ETA: 0:19:01 Progress: 3%|█▎ | ETA: 0:18:52 Progress: 3%|█▍ | ETA: 0:18:45 Progress: 4%|█▋ | ETA: 0:18:35 Progress: 4%|█▊ | ETA: 0:18:28 Progress: 5%|██ | ETA: 0:18:25 Progress: 5%|██▏ | ETA: 0:18:20 Progress: 6%|██▍ | ETA: 0:18:14 Progress: 6%|██▌ | ETA: 0:18:14 Progress: 7%|██▋ | ETA: 0:18:11 Progress: 7%|██▉ | ETA: 0:18:04 Progress: 7%|███ | ETA: 0:17:59 Progress: 8%|███▎ | ETA: 0:17:56 Progress: 8%|███▍ | ETA: 0:17:50 Progress: 9%|███▋ | ETA: 0:17:40 Progress: 9%|███▊ | ETA: 0:17:32 Progress: 10%|████ | ETA: 0:17:23 Progress: 10%|████▏ | ETA: 0:17:14 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 331 running 1 of 1 signal (10): User defined signal 1 unknown function (ip: 0x756ac99c04f3) at /lib/x86_64-linux-gnu/libc.so.6 ijl_egal__bitstag at /source/src/builtins.c:286 [inlined] ijl_egal__bitstag at /source/src/builtins.c:245 == at ./strings/string.jl:187 [inlined] isequal at ./operators.jl:178 [inlined] #_#59 at ./operators.jl:1203 [inlined] Fix at ./operators.jl:1203 [inlined] findnext at ./array.jl:2449 [inlined] findfirst at ./array.jl:2500 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:74 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:44 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x756aa11283d6) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 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:1961 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_invoke at /source/src/gf.c:4123 jl_toplevel_eval_flex at /source/src/toplevel.c:731 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:3003 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3063 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x756aa89103a2) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [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:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:3003 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3063 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_76447.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [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:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_73111.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [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: 0x756ac9895249) 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: 91%|█████████████████████████████████████▎ | ETA: 0:01:47 ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ====================================================================================== 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_41502.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [inlined] start_task at /source/src/task.c:1272 unknown function (ip: (nil)) at (unknown file) Progress: 91%|█████████████████████████████████████▍ | ETA: 0:01:42 ============================================================== 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 0x000072a85dd871c0 Total snapshots: 391. Utilization: 0% ╎391 @Base/task.jl:1168 wait_forever() 390╎ 391 @Base/task.jl:1246 wait() ┌ 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 0x0000756aaf7fc010 Total snapshots: 542. Utilization: 100% ╎542 @Base/client.jl:577 _start() ╎ 542 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 542 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 542 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 542 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 542 @Base/loading.jl:3063 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 542 @Base/loading.jl:3003 include_string(mapexpr::typeof(identity), m… ╎ ╎ 542 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 542 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 542 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 542 @Base/loading.jl:3063 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 542 @Base/loading.jl:3003 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 542 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 542 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 542 @Test/src/Test.jl:1961 macro expansion ╎ ╎ ╎ 542 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 542 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 5╎ ╎ ╎ ╎ 86 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 7 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 7 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:125 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex 1╎ ╎ ╎ ╎ 4 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:964 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:385 checkbounds ╎ ╎ ╎ ╎ ╎ 2 @Base/…ators.jl:424 > 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < ╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 66 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 65 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ 64 @Base/array.jl:2449 findnext 6╎ ╎ ╎ ╎ ╎ 6 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 58 @Base/…ators.jl:1203 Fix ╎ ╎ ╎ ╎ ╎ 58 @Base/…tors.jl:1203 #_#59 ╎ ╎ ╎ ╎ ╎ 58 @Base/…tors.jl:178 isequal 57╎ ╎ ╎ ╎ ╎ 58 @Base/…ring.jl:187 == ╎ ╎ ╎ ╎ 1 @Base/array.jl:2450 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 3 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:2449 findnext ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 #findgenokey##0 1╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:673 isequaldata 2╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex 1╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:225 geno_ismissing 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:82 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3196 getindex ╎ ╎ ╎ ╎ 1 @Base/range.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:943 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:83 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:381 checkbounds ╎ ╎ ╎ ╎ 456 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 456 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 64 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 64 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 64 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2125 empty! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1288 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:211 _unsetindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:596 memoryref ╎ ╎ ╎ ╎ ╎ 42 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 33 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 12 @Base/array.jl:436 getindex 12╎ ╎ ╎ ╎ ╎ 12 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 19 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 18 @Base/…ray.jl:1348 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1197 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1204 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 2╎ ╎ ╎ ╎ ╎ ╎ 15 @Base/…ray.jl:1205 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1180 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1096 overallocation ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ay.jl:1101 array_new_memory 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ot.jl:588 GenericMemory 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1189 _growend_internal!(a::Vect… 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1190 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1349 _push! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1044 __safe_setindex! ╎ ╎ ╎ ╎ ╎ 1 @Base/…cast.jl:1352 broadcasted ╎ ╎ ╎ ╎ ╎ 1 @Base/…ast.jl:1156 broadcasted ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:159 range ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:159 #range#30 ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:175 _range ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:220 range_start_stop ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:5 Colon ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:417 UnitRange ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ge.jl:428 unitrange_last ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…rs.jl:479 >= 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:464 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Base/…tors.jl:424 > 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:572 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…yops.jl:51 vload ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…sics.jl:477 load 2╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:486 macro expansion 2╎ ╎ ╎ ╎ ╎ 3 @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 1╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:584 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1454 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 20 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 20 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 20 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 20 @BufferedStreams/…:5 readbytes! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1167 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/io.jl:1168 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 11 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 11 @TranscodingStreams/…:302 peek 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:964 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:381 checkbounds 9╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ls.jl:965 getindex ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/io.jl:1170 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ors.jl:424 > 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/io.jl:1174 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ray.jl:393 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ay.jl:1020 setindex! 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 392 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 392 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 392 @Base/…epcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 1 @Base/…pcopy.jl:132 deepcopy_internal(x::Vector{V… 1╎ ╎ ╎ ╎ ╎ 1 @Base/iddict.jl:86 setindex! ╎ ╎ ╎ ╎ ╎ 391 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:107 _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 390 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… ╎ ╎ ╎ ╎ ╎ 390 @Base/…copy.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:0 _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:594 memoryref 49╎ ╎ ╎ ╎ ╎ 49 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 9╎ ╎ ╎ ╎ ╎ 9 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 9╎ ╎ ╎ ╎ ╎ 9 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 17╎ ╎ ╎ ╎ ╎ 281 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ct.jl:182 in 27╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 37 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:661 Array 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ot.jl:649 Array 33╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ict.jl:86 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 199 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… ╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…ct.jl:182 in 66╎ ╎ ╎ ╎ ╎ ╎ 66 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 129 @Base/…opy.jl:142 deepcopy_internal(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:0 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:182 in 21╎ ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:92 get 12╎ ╎ ╎ ╎ ╎ ╎ 106 @Base/…py.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:108 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:876 isbitstype 18╎ ╎ ╎ ╎ ╎ ╎ 89 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:189 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ry.jl:193 copy(a::Memory{UnitRange… 29╎ ╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ot.jl:588 GenericMemory 1╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ry.jl:194 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ry.jl:157 unsafe_copyto! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ry.jl:139 unsafe_copyto! 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…em.jl:28 memmove 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:81 setindex! 33╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ct.jl:86 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 23╎ ╎ ╎ ╎ ╎ 23 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 14╎ ╎ ╎ ╎ ╎ 14 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:125 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:925 iterate [331] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 unknown function (ip: 0x756ac99c02c1) at /lib/x86_64-linux-gnu/libc.so.6 ijl_egal__bitstag at /source/src/builtins.c:286 [inlined] ijl_egal__bitstag at /source/src/builtins.c:245 == at ./strings/string.jl:187 [inlined] isequal at ./operators.jl:178 [inlined] #_#59 at ./operators.jl:1203 [inlined] Fix at ./operators.jl:1203 [inlined] findnext at ./array.jl:2449 [inlined] findfirst at ./array.jl:2500 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:74 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:44 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x756aa11283d6) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 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:1961 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_invoke at /source/src/gf.c:4123 jl_toplevel_eval_flex at /source/src/toplevel.c:731 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:3003 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3063 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x756aa89103a2) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [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:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:3003 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3063 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_76447.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [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:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_73111.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2284 [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: 0x756ac9895249) 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: 18072027782 (Pool: 18072012063; Big: 15719); GC: 21766 PkgEval terminated after 2722.4s: test duration exceeded the time limit