Package evaluation of VCFTools on Julia 1.13.0-DEV.1080 (ed57414aec*) started at 2025-09-04T18:18:31.893 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 11.05s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed CompositionsBase ──────── v0.1.2 Installed FillArrays ────────────── v1.13.0 Installed CommonSolve ───────────── v0.2.4 Installed Rmath_jll ─────────────── v0.5.1+0 Installed DelimitedFiles ────────── v1.9.1 Installed MacroTools ────────────── v0.5.16 Installed AliasTables ───────────── v1.1.3 Installed HypergeometricFunctions ─ v0.3.28 Installed ConstructionBase ──────── v1.6.0 Installed CodecZlib ─────────────── v0.7.8 Installed VCFTools ──────────────── v0.2.10 Installed DataStructures ────────── v0.19.1 Installed StatsBase ─────────────── v0.34.6 Installed TranscodingStreams ────── v0.11.3 Installed SIMD ──────────────────── v3.7.1 Installed Combinatorics ─────────── v1.0.3 Installed DataAPI ───────────────── v1.16.0 Installed OrderedCollections ────── v1.8.1 Installed StatsAPI ──────────────── v1.7.1 Installed Statistics ────────────── v1.11.1 Installed HypothesisTests ───────── v0.11.5 Installed PrecompileTools ───────── v1.3.3 Installed IrrationalConstants ───── v0.2.4 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed ProgressMeter ─────────── v1.11.0 Installed BufferedStreams ───────── v1.2.2 Installed LogExpFunctions ───────── v0.3.29 Installed QuadGK ────────────────── v2.11.2 Installed Roots ─────────────────── v2.2.10 Installed Rmath ─────────────────── v0.8.0 Installed BioGenerics ───────────── v0.1.5 Installed PtrArrays ─────────────── v1.3.0 Installed StatsFuns ─────────────── v1.5.0 Installed InverseFunctions ──────── v0.1.17 Installed SpecialFunctions ──────── v2.5.1 Installed Distributions ─────────── v0.25.120 Installed Reexport ──────────────── v1.2.2 Installed Preferences ───────────── v1.5.0 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed PDMats ────────────────── v0.11.35 Installed BGZFStreams ───────────── v0.3.2 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.42 Installed Automa ────────────────── v1.1.0 Installed VariantCallFormat ─────── v0.5.7 Installed SortingAlgorithms ─────── v1.2.2 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/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 v0.19.1 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [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 v0.11.35 [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 v0.8.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.1 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.7 [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 v0.7.0 [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 v5.13.1+0 Installation completed after 8.31s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4846.2 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 392.87s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_sqXtNn/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.6 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [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_sqXtNn/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 v4.18.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.1 [864edb3b] DataStructures v0.19.1 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [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 v0.11.35 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 ⌅ [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [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 v0.6.4 [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 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [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 v8.15.0+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.8.12 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.2+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 v5.13.1+0 [8e850ede] nghttp2_jll v1.67.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.5s Test Summary: | Pass Total Time openvcf | 4 4 2.5s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.7s 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: 0:33:00 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 14.801798 seconds (10.93 M allocations: 686.430 MiB, 4.47% gc time, 96.38% compilation time: 18% of which was recompilation) 0.477405 seconds (2.86 M allocations: 195.805 MiB, 11.05% gc time, 20.88% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:29:46 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.138843 seconds (4.55 M allocations: 309.930 MiB, 2.14% gc time, 85.12% compilation time) 0.469583 seconds (2.85 M allocations: 195.488 MiB, 5.16% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 22.7s 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 2.0s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.3s 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 6.4s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:29 Progress: 0%|▏ | ETA: 0:19:44 Progress: 0%|▏ | ETA: 0:19:14 Progress: 0%|▏ | ETA: 0:19:05 Progress: 0%|▏ | ETA: 0:18:51 Progress: 1%|▎ | ETA: 0:18:40 Progress: 1%|▎ | ETA: 0:18:34 Progress: 1%|▎ | ETA: 0:18:31 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100%|█████████████████████████████████████████| Time: 0:01:42 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 16:39:08 Progress: 24%|██████████ | ETA: 0:04:37 Progress: 45%|██████████████████▋ | ETA: 0:01:49 Progress: 65%|██████████████████████████▊ | ETA: 0:00:49 Progress: 93%|██████████████████████████████████████ | ETA: 0:00:07 Progress: 100%|█████████████████████████████████████████| Time: 0:01:33 [ Info: 823 records are matched 206.072891 seconds (2.19 G allocations: 143.742 GiB, 6.42% gc time, 0.49% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:12:45 Progress: 0%|▏ | ETA: 0:12:31 Progress: 0%|▏ | ETA: 0:12:22 Progress: 1%|▎ | ETA: 0:12:44 Progress: 1%|▎ | ETA: 0:12:35 Progress: 1%|▍ | ETA: 0:12:29 Progress: 1%|▍ | ETA: 0:12:25 Progress: 1%|▌ | ETA: 0:12:23 Progress: 1%|▌ | ETA: 0:12:20 Progress: 1%|▌ | ETA: 0:12:17 Progress: 2%|▋ | ETA: 0:12:17 Progress: 2%|▋ | ETA: 0:12:21 Progress: 2%|▊ | ETA: 0:12:20 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ETA: 0:12:03 Progress: 10%|████ | ETA: 0:12:01 Progress: 10%|████▏ | ETA: 0:11:59 Progress: 10%|████▏ | ETA: 0:11:57 Progress: 10%|████▎ | ETA: 0:11:55 Progress: 100%|█████████████████████████████████████████| Time: 0:01:22 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 15:08:32 Progress: 29%|███████████▉ | ETA: 0:03:21 Progress: 57%|███████████████████████▌ | ETA: 0:01:02 Progress: 88%|███████████████████████████████████▉ | ETA: 0:00:12 Progress: 100%|█████████████████████████████████████████| Time: 0:01:23 [ Info: 488 records are matched 174.630898 seconds (2.19 G allocations: 143.726 GiB, 7.06% gc time, 0.41% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:34 Progress: 0%|▏ | ETA: 0:17:16 Progress: 0%|▏ | ETA: 0:15:21 Progress: 0%|▏ | ETA: 0:14:37 Progress: 1%|▎ | ETA: 0:14:02 Progress: 1%|▎ | ETA: 0:13:42 Progress: 1%|▍ | ETA: 0:13:26 Progress: 1%|▍ | ETA: 0:13:13 Progress: 1%|▌ | ETA: 0:13:07 Progress: 1%|▌ | ETA: 0:12:59 Progress: 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10%|████ | ETA: 0:11:39 Progress: 10%|████ | ETA: 0:11:38 Progress: 10%|████▏ | ETA: 0:11:37 Progress: 10%|████▏ | ETA: 0:11:37 Progress: 10%|████▎ | ETA: 0:11:35 Progress: 100%|█████████████████████████████████████████| Time: 0:01:19 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:17:06 Progress: 20%|████████▏ | ETA: 0:07:02 Progress: 39%|████████████████▏ | ETA: 0:02:41 Progress: 61%|████████████████████████▉ | ETA: 0:01:09 Progress: 82%|█████████████████████████████████▋ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: 0 records are matched 196.188930 seconds (2.19 G allocations: 143.726 GiB, 6.84% gc time, 0.31% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 9m43.4s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 16:56:28 Progress: 28%|███████████▋ | ETA: 0:03:51 Progress: 56%|███████████████████████▏ | ETA: 0:01:12 Progress: 80%|████████████████████████████████▉ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:34 [ Info: 833 records are matched 104.590354 seconds (1.11 G allocations: 72.816 GiB, 6.59% gc time, 0.58% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:24:21 Progress: 19%|███████▉ | ETA: 0:07:37 Progress: 39%|███████████████▉ | ETA: 0:02:54 Progress: 60%|████████████████████████▍ | ETA: 0:01:16 Progress: 82%|█████████████████████████████████▊ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: 493 records are matched 122.905191 seconds (1.11 G allocations: 72.816 GiB, 6.13% gc time, 0.51% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:25:40 Progress: 20%|████████▏ | ETA: 0:07:21 Progress: 40%|████████████████▍ | ETA: 0:02:46 Progress: 62%|█████████████████████████▍ | ETA: 0:01:09 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: 0 records are matched 123.820789 seconds (1.11 G allocations: 72.816 GiB, 6.04% gc time, 0.49% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m53.7s 1.168031 seconds (1.28 M allocations: 91.106 MiB, 4.75% gc time, 84.29% compilation time) 0.997600 seconds (1.16 M allocations: 86.522 MiB, 76.97% compilation time) 0.939646 seconds (1.16 M allocations: 85.784 MiB, 4.56% gc time, 80.85% compilation time) 0.423967 seconds (203.58 k allocations: 11.537 MiB, 99.97% compilation time) 0.010518 seconds (6.25 k allocations: 484.477 KiB, 96.38% compilation time) 0.009890 seconds (2.65 k allocations: 247.602 KiB, 96.41% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.7s 0.982256 seconds (952.40 k allocations: 74.461 MiB, 4.16% gc time, 76.90% compilation time) 0.831644 seconds (859.94 k allocations: 71.480 MiB, 2.91% gc time, 76.45% 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 0.121825 seconds (525.29 k allocations: 50.448 MiB, 13.91% gc time, 27.59% compilation time) 0.665655 seconds (647.50 k allocations: 57.700 MiB, 1.91% gc time, 86.86% 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 0.555115 seconds (520.49 k allocations: 51.920 MiB, 86.82% gc time, 1.75% compilation time: <1% of which was recompilation) 0.557263 seconds (589.76 k allocations: 56.005 MiB, 84.46% 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 0.127036 seconds (1.56 M allocations: 81.839 MiB, 6.82% compilation time) 0.628047 seconds (1.70 M allocations: 90.355 MiB, 4.97% gc time, 73.78% 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 7.3s Test Summary: | Pass Total Time record info | 14 14 5.1s Test Summary: | Pass Total Time write VCF | 3 3 3.8s 2.224306 seconds (5.28 M allocations: 380.121 MiB, 3.64% gc time, 52.86% compilation time) 1.652939 seconds (2.86 M allocations: 194.788 MiB, 2.43% gc time, 13.77% compilation time) 1.318141 seconds (4.89 M allocations: 358.312 MiB, 4.03% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 8.0s 1.451065 seconds (617.03 k allocations: 54.318 MiB, 0.90% gc time, 34.28% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.1s Test Summary: | Pass Total Time filter_chr | 4 4 1.8s Progress: 0%|▏ | ETA: 0:21:24 Progress: 1%|▍ | ETA: 0:20:49 Progress: 1%|▌ | ETA: 0:20:38 Progress: 2%|▋ | ETA: 0:20:04 Progress: 2%|▉ | ETA: 0:19:59 Progress: 2%|█ | ETA: 0:19:58 Progress: 3%|█▏ | ETA: 0:20:01 Progress: 3%|█▍ | ETA: 0:20:00 Progress: 4%|█▌ | ETA: 0:19:56 Progress: 4%|█▋ | ETA: 0:19:52 Progress: 4%|█▉ | ETA: 0:19:49 Progress: 5%|██ | ETA: 0:19:44 Progress: 5%|██▏ | ETA: 0:19:40 Progress: 6%|██▍ | ETA: 0:19:35 Progress: 6%|██▌ | ETA: 0:19:23 Progress: 7%|██▊ | ETA: 0:19:18 Progress: 7%|██▉ | ETA: 0:19:13 Progress: 7%|███ | ETA: 0:19:10 Progress: 8%|███▏ | ETA: 0:19:06 Progress: 8%|███▍ | ETA: 0:19:00 Progress: 9%|███▌ | ETA: 0:18:53 Progress: 9%|███▊ | ETA: 0:18:49 Progress: 9%|███▉ | ETA: 0:18:44 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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 433 running 1 of 1 signal (10): User defined signal 1 setproperty! at ./Base_compiler.jl:61 [inlined] setindex! at ./iddict.jl:86 [inlined] _deepcopy_memory_t at ./deepcopy.jl:109 _jl_invoke at /source/src/gf.c:4001 [inlined] ijl_invoke at /source/src/gf.c:4008 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x7103d5b5c146) at (unknown file) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 _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/DDn3I/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: 0x7103b0b328a6) at (unknown file) _jl_invoke at /source/src/gf.c:4001 [inlined] ijl_apply_generic at /source/src/gf.c:4198 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.13/Test/src/Test.jl:1952 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4001 [inlined] ijl_invoke at /source/src/gf.c:4008 jl_toplevel_eval_flex at /source/src/toplevel.c:761 jl_toplevel_eval_flex at /source/src/toplevel.c:712 ijl_toplevel_eval at /source/src/toplevel.c:784 ijl_toplevel_eval_in at /source/src/toplevel.c:829 eval at ./boot.jl:489 include_string at ./loading.jl:2865 _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 _include at ./loading.jl:2925 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_36079.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 jl_apply at /source/src/julia.h:2382 [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:690 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:772 jl_toplevel_eval_flex at /source/src/toplevel.c:712 ijl_toplevel_eval at /source/src/toplevel.c:784 ijl_toplevel_eval_in at /source/src/toplevel.c:829 eval at ./boot.jl:489 include_string at ./loading.jl:2865 _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 _include at ./loading.jl:2925 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_36079.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 jl_apply at /source/src/julia.h:2382 [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:690 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:772 jl_toplevel_eval_flex at /source/src/toplevel.c:712 ijl_toplevel_eval at /source/src/toplevel.c:784 ijl_toplevel_eval_in at /source/src/toplevel.c:829 eval at ./boot.jl:489 exec_options at ./client.jl:296 _start at ./client.jl:563 jfptr__start_63312.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 jl_apply at /source/src/julia.h:2382 [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: 0x7103d7420249) 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) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Progress: 95%|███████████████████████████████████████ | ETA: 0:00:59┌ 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007103bd5fc010 Total snapshots: 584. Utilization: 100% ╎583 @Base/client.jl:563 _start() ╎ 583 @Base/client.jl:296 exec_options(opts::Base.JLOptions) ╎ 583 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 583 @Base/Base.jl:310 (::Base.IncludeInto)(fname::String) ╎ 583 @Base/Base.jl:309 include(mapexpr::Function, mod::Module, _path::St… ╎ 583 @Base/loading.jl:2925 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 583 @Base/loading.jl:2865 include_string(mapexpr::typeof(identity), m… ╎ ╎ 583 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 583 @Base/Base.jl:310 (::Base.IncludeInto)(fname::String) ╎ ╎ 583 @Base/Base.jl:309 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 583 @Base/loading.jl:2925 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 583 @Base/loading.jl:2865 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 583 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 583 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 583 @Test/src/Test.jl:1952 macro expansion ╎ ╎ ╎ 583 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 583 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 81 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 1 @Base/array.jl:995 setindex! 1╎ ╎ ╎ ╎ 1 @Base/array.jl:1000 _setindex! 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:0 aim_select(record::VariantCallForm… ╎ ╎ ╎ ╎ 1 @VCFTools/…ct.jl:60 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 @Base/array.jl:334 fill! ╎ ╎ ╎ ╎ 1 @Base/array.jl:338 _fill! ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:995 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1000 _setindex! ╎ ╎ ╎ ╎ 10 @VCFTools/…ct.jl:65 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 10 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 7 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 3 @Base/…ators.jl:425 > 3╎ ╎ ╎ ╎ ╎ 3 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 2 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:964 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:381 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 54 @VCFTools/…ct.jl:74 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 52 @Base/array.jl:2465 findfirst 1╎ ╎ ╎ ╎ 51 @Base/array.jl:2414 findnext 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 47 @Base/…ators.jl:1195 Fix ╎ ╎ ╎ ╎ ╎ 47 @Base/…tors.jl:1195 #_#59 ╎ ╎ ╎ ╎ ╎ 47 @Base/…tors.jl:178 isequal 47╎ ╎ ╎ ╎ ╎ 47 @Base/…ring.jl:186 == ╎ ╎ ╎ ╎ 1 @Base/array.jl:2415 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 4 @VCFTools/…ct.jl:76 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 4 @VariantCallFormat/…:613 findgenokey 1╎ ╎ ╎ ╎ 1 @Base/…piler.jl:57 getproperty ╎ ╎ ╎ ╎ 3 @Base/array.jl:2465 findfirst ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:2414 findnext ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:673 isequaldata 3╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 2 @VCFTools/…ct.jl:79 aim_select(record::VariantCallFor… 2╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:225 geno_ismissing ╎ ╎ ╎ ╎ 2 @VCFTools/…ct.jl:83 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 2 @Base/array.jl:3161 getindex ╎ ╎ ╎ ╎ 2 @Base/range.jl:954 _getindex 2╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:941 _in_unit_range ╎ ╎ ╎ ╎ 2 @VCFTools/…ct.jl:85 aim_select(record::VariantCallFor… 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 2 @VCFTools/…ct.jl:86 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 @Base/array.jl:995 setindex! 1╎ ╎ ╎ ╎ 1 @Base/array.jl:1000 _setindex! 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ct.jl:99 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 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/…ct.jl:109 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 + ╎ ╎ ╎ ╎ 502 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 502 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 77 @BioGenerics/…jl:87 iterate 1╎ ╎ ╎ ╎ 1 @BioGenerics/…jl:75 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ 76 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 76 @VariantCallFormat/…:142 read!(reader::VariantCall… 1╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:145 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2090 empty! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1253 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:218 _unsetindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:596 memoryref ╎ ╎ ╎ ╎ ╎ 57 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 53 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 13 @Base/array.jl:411 getindex 13╎ ╎ ╎ ╎ ╎ 13 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 39 @Base/array.jl:1310 push! ╎ ╎ ╎ ╎ ╎ 38 @Base/…ray.jl:1313 _push! ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ray.jl:1176 _growend! 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1180 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 3╎ ╎ ╎ ╎ ╎ ╎ 32 @Base/…ray.jl:1181 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1133 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 19 @Base/…ay.jl:1156 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 19 @Base/…ay.jl:1076 array_new_memory 19╎ ╎ ╎ ╎ ╎ ╎ 19 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1159 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:595 memoryref 8╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ay.jl:1165 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1314 _push! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 __safe_setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:0 getindex ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:503 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1452 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…dvec.jl:481 all ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…dvec.jl:476 reduce ╎ ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…ics.jl:832 reduce_and 1╎ ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…ics.jl:847 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:583 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:56 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:49 checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:584 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1452 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 17 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 17 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 17 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 17 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/io.jl:1160 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @CodecZlib/…:195 process(codec::GzipDec… 6╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/io.jl:1161 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 8 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/io.jl:359 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:298 peek 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:209 eof ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:302 peek ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:964 getindex 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:385 checkbounds 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ls.jl:965 getindex ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/io.jl:1167 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:399 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:995 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:999 _setindex! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ay.jl:1000 _setindex! ╎ ╎ ╎ ╎ 425 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 425 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:359 copy 2╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 423 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 423 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:138 deepcopy_internal(x::MemoryRe… ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:182 in 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:92 get ╎ ╎ ╎ ╎ ╎ 422 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 5╎ ╎ ╎ ╎ ╎ 422 @Base/…copy.jl:104 deepcopy_internal 47╎ ╎ ╎ ╎ ╎ 47 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 11╎ ╎ ╎ ╎ ╎ 11 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 9╎ ╎ ╎ ╎ ╎ 9 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 3╎ ╎ ╎ ╎ ╎ 3 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 20╎ ╎ ╎ ╎ ╎ 300 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:128 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 35 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 35 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 35 @Base/…ct.jl:182 in 34╎ ╎ ╎ ╎ ╎ ╎ 35 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 35 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:661 Array 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ot.jl:649 Array 29╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ict.jl:86 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 207 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ct.jl:182 in 63╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 132 @Base/…opy.jl:142 deepcopy_internal(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:0 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:182 in 24╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ct.jl:92 get 5╎ ╎ ╎ ╎ ╎ ╎ 106 @Base/…py.jl:104 deepcopy_internal 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 7╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:108 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:868 isbitstype 14╎ ╎ ╎ ╎ ╎ ╎ 91 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ry.jl:175 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ry.jl:179 copy(a::Memory{UnitRange… 23╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ry.jl:180 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ry.jl:143 unsafe_copyto! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ry.jl:125 unsafe_copyto! 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…em.jl:28 memmove 1╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ct.jl:81 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:88 * 40╎ ╎ ╎ ╎ ╎ ╎ 42 @Base/…ct.jl:86 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:144 deepcopy_internal(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…on.jl:637 == 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…opy.jl:145 deepcopy_internal(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 35╎ ╎ ╎ ╎ ╎ 35 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 12╎ ╎ ╎ ╎ ╎ 12 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ====================================================================================== 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:1200 wait_forever at ./task.jl:1137 jfptr_wait_forever_44650.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 jl_apply at /source/src/julia.h:2382 [inlined] start_task at /source/src/task.c:1253 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000072061612b1c0 Total snapshots: 365. Utilization: 0% ╎365 @Base/task.jl:1137 wait_forever() 364╎ 365 @Base/task.jl:1200 wait() [433] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 Array at ./boot.jl:649 [inlined] Array at ./boot.jl:661 [inlined] deepcopy_internal at ./deepcopy.jl:132 unknown function (ip: 0x7103d5b5c146) at (unknown file) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 _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/DDn3I/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: 0x7103b0b328a6) at (unknown file) _jl_invoke at /source/src/gf.c:4001 [inlined] ijl_apply_generic at /source/src/gf.c:4198 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.13/Test/src/Test.jl:1952 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4001 [inlined] ijl_invoke at /source/src/gf.c:4008 jl_toplevel_eval_flex at /source/src/toplevel.c:761 jl_toplevel_eval_flex at /source/src/toplevel.c:712 ijl_toplevel_eval at /source/src/toplevel.c:784 ijl_toplevel_eval_in at /source/src/toplevel.c:829 eval at ./boot.jl:489 include_string at ./loading.jl:2865 _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 _include at ./loading.jl:2925 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_36079.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 jl_apply at /source/src/julia.h:2382 [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:690 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:772 jl_toplevel_eval_flex at /source/src/toplevel.c:712 ijl_toplevel_eval at /source/src/toplevel.c:784 ijl_toplevel_eval_in at /source/src/toplevel.c:829 eval at ./boot.jl:489 include_string at ./loading.jl:2865 _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 _include at ./loading.jl:2925 include at ./Base.jl:309 IncludeInto at ./Base.jl:310 jfptr_IncludeInto_36079.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 jl_apply at /source/src/julia.h:2382 [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:690 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:772 jl_toplevel_eval_flex at /source/src/toplevel.c:712 ijl_toplevel_eval at /source/src/toplevel.c:784 ijl_toplevel_eval_in at /source/src/toplevel.c:829 eval at ./boot.jl:489 exec_options at ./client.jl:296 _start at ./client.jl:563 jfptr__start_63312.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3985 [inlined] ijl_apply_generic at /source/src/gf.c:4198 jl_apply at /source/src/julia.h:2382 [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: 0x7103d7420249) 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: 20100258232 (Pool: 20100242736; Big: 15496); GC: 35061 PkgEval terminated after 2721.63s: test duration exceeded the time limit