Package evaluation of VCFTools on Julia 1.13.0-DEV.1277 (fa66b63fc3*) started at 2025-10-08T04:11:51.868 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.96s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... 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 v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.14.0 [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 v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [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 v5.15.0+0 Installation completed after 5.8s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5301.6 ms ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 195.76s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_B8CpxJ/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [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_B8CpxJ/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 v1.8.0 [864edb3b] DataStructures v0.19.1 [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 v1.14.0 [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 v3.0.11 [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 v3.7.2 [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 v0.34.6 [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 [3fa0cd96] REPL 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 v8.16.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [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 v1.67.1+0 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 9.6s Test Summary: | Pass Total Time openvcf | 4 4 6.4s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.4s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.2s ┌ 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: 0:33:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 14.107971 seconds (10.35 M allocations: 582.492 MiB, 1.62% gc time, 96.16% compilation time: 20% of which was recompilation) 0.466078 seconds (2.40 M allocations: 143.633 MiB, 12.07% gc time, 17.60% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:31:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.380205 seconds (4.11 M allocations: 243.074 MiB, 3.39% gc time, 84.97% compilation time) 0.475827 seconds (2.38 M allocations: 143.408 MiB) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 22.8s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.9s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 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 5.7s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:12 Progress: 0%|▏ | ETA: 0:17:49 Progress: 0%|▏ | ETA: 0:17:43 Progress: 0%|▏ | ETA: 0:17:38 Progress: 0%|▎ | ETA: 0:17:34 Progress: 1%|▎ | ETA: 0:17:32 Progress: 1%|▎ | ETA: 0:17:28 Progress: 1%|▍ | ETA: 0:17:25 Progress: 1%|▍ 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reference IDs Progress: 0%| | ETA: 18:51:55 Progress: 20%|████████▏ | ETA: 0:06:49 Progress: 40%|████████████████▍ | ETA: 0:02:34 Progress: 62%|█████████████████████████▎ | ETA: 0:01:04 Progress: 83%|██████████████████████████████████▏ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 488 records are matched 219.447890 seconds (2.01 G allocations: 106.121 GiB, 5.63% gc time, 0.39% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:26 Progress: 0%|▏ | ETA: 0:18:00 Progress: 0%|▏ | ETA: 0:17:46 Progress: 0%|▏ | ETA: 0:17:42 Progress: 0%|▎ | ETA: 0:17:33 Progress: 1%|▎ | ETA: 0:17:28 Progress: 1%|▎ | ETA: 0:17:25 Progress: 1%|▍ | ETA: 0:17:24 Progress: 1%|▍ | ETA: 0:17:21 Progress: 1%|▍ | ETA: 0:17:19 Progress: 1%|▍ | ETA: 0:17:17 Progress: 1%|▌ | ETA: 0:17:14 Progress: 1%|▌ | ETA: 0:17:13 Progress: 1%|▌ | ETA: 0:17:13 Progress: 1%|▋ | ETA: 0:17:10 Progress: 2%|▋ | ETA: 0:17:06 Progress: 2%|▋ | ETA: 0:17:01 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| ETA: 0:15:21 Progress: 8%|███▍ | ETA: 0:15:20 Progress: 8%|███▌ | ETA: 0:15:20 Progress: 9%|███▌ | ETA: 0:15:19 Progress: 9%|███▌ | ETA: 0:15:18 Progress: 9%|███▋ | ETA: 0:15:18 Progress: 9%|███▋ | ETA: 0:15:15 Progress: 9%|███▋ | ETA: 0:15:09 Progress: 9%|███▊ | ETA: 0:15:02 Progress: 9%|███▊ | ETA: 0:14:56 Progress: 9%|███▉ | ETA: 0:14:50 Progress: 10%|███▉ | ETA: 0:14:44 Progress: 10%|████ | ETA: 0:14:38 Progress: 10%|████ | ETA: 0:14:32 Progress: 10%|████▏ | ETA: 0:14:26 Progress: 10%|████▏ | ETA: 0:14:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:38 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:35:58 Progress: 22%|█████████▏ | ETA: 0:05:52 Progress: 43%|█████████████████▊ | ETA: 0:02:12 Progress: 65%|██████████████████████████▋ | ETA: 0:00:55 Progress: 88%|███████████████████████████████████▉ | ETA: 0:00:15 Progress: 100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: 0 records are matched 212.783410 seconds (2.01 G allocations: 106.120 GiB, 5.74% gc time, 0.42% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m03.0s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:05:01 Progress: 19%|███████▊ | ETA: 0:07:18 Progress: 39%|███████████████▉ | ETA: 0:02:45 Progress: 60%|████████████████████████▊ | ETA: 0:01:08 Progress: 83%|██████████████████████████████████ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 833 records are matched 116.767660 seconds (1.02 G allocations: 53.885 GiB, 5.66% gc time, 0.52% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:59:33 Progress: 20%|████████▎ | ETA: 0:07:08 Progress: 41%|████████████████▊ | ETA: 0:02:38 Progress: 62%|█████████████████████████▍ | ETA: 0:01:07 Progress: 85%|██████████████████████████████████▋ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: 493 records are matched 121.408063 seconds (1.02 G allocations: 53.884 GiB, 5.51% gc time, 0.46% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:33:58 Progress: 20%|████████▍ | ETA: 0:06:49 Progress: 42%|█████████████████▎ | ETA: 0:02:26 Progress: 64%|██████████████████████████▍ | ETA: 0:00:59 Progress: 87%|███████████████████████████████████▊ | ETA: 0:00:16 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: 0 records are matched 119.224088 seconds (1.02 G allocations: 53.885 GiB, 5.59% gc time, 0.50% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m59.6s 1.174904 seconds (1.29 M allocations: 69.691 MiB, 4.37% gc time, 80.94% compilation time) 0.940233 seconds (1.19 M allocations: 66.177 MiB, 81.29% compilation time) 1.007313 seconds (1.19 M allocations: 65.200 MiB, 3.24% gc time, 77.11% compilation time) 0.416544 seconds (211.84 k allocations: 11.122 MiB, 99.96% compilation time) 0.011513 seconds (6.38 k allocations: 392.242 KiB, 96.60% compilation time) 0.008707 seconds (2.65 k allocations: 165.508 KiB, 96.40% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.4s 0.880426 seconds (979.12 k allocations: 54.657 MiB, 81.11% compilation time) 0.878135 seconds (878.22 k allocations: 51.615 MiB, 4.00% gc time, 76.45% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.3s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.129610 seconds (525.51 k allocations: 30.680 MiB, 17.26% gc time, 22.16% compilation time) 0.612103 seconds (651.44 k allocations: 37.706 MiB, 88.05% 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 0.081886 seconds (520.58 k allocations: 32.160 MiB, 18.15% gc time) 0.514526 seconds (594.59 k allocations: 36.351 MiB, 86.77% 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 0.132994 seconds (1.56 M allocations: 62.080 MiB, 13.28% gc time, 6.10% compilation time) 0.581176 seconds (1.71 M allocations: 70.291 MiB, 3.19% gc time, 77.85% 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 6.4s Test Summary: | Pass Total Time record info | 14 14 5.2s Test Summary: | Pass Total Time write VCF | 3 3 4.2s 2.220801 seconds (4.80 M allocations: 296.449 MiB, 3.52% gc time, 55.26% compilation time) 1.004247 seconds (2.39 M allocations: 142.773 MiB, 3.97% gc time, 22.73% compilation time) 0.938227 seconds (4.42 M allocations: 276.644 MiB, 4.63% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.0s 1.267816 seconds (609.73 k allocations: 33.704 MiB, 1.24% gc time, 35.81% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.2s Test Summary: | Pass Total Time filter_chr | 4 4 1.6s Progress: 0%|▏ | ETA: 0:20:35 Progress: 1%|▍ | ETA: 0:20:22 Progress: 1%|▌ | ETA: 0:20:29 Progress: 2%|▋ | ETA: 0:20:25 Progress: 2%|▉ | ETA: 0:20:15 Progress: 2%|█ | ETA: 0:20:16 Progress: 3%|█▏ | ETA: 0:20:13 Progress: 3%|█▍ | ETA: 0:20:01 Progress: 4%|█▌ | ETA: 0:19:55 Progress: 4%|█▋ | ETA: 0:19:53 Progress: 4%|█▉ | ETA: 0:19:52 Progress: 5%|██ | ETA: 0:19:50 Progress: 5%|██▏ | ETA: 0:19:45 Progress: 6%|██▍ | ETA: 0:19:38 Progress: 6%|██▌ | ETA: 0:19:36 Progress: 6%|██▋ | ETA: 0:19:31 Progress: 7%|██▉ | ETA: 0:19:29 Progress: 7%|███ | ETA: 0:19:28 Progress: 8%|███▏ | ETA: 0:19:24 Progress: 8%|███▎ | ETA: 0:19:19 Progress: 8%|███▌ | ETA: 0:19:13 Progress: 9%|███▋ | ETA: 0:19:07 Progress: 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69%|████████████████████████████▍ | ETA: 0:06:26 Progress: 70%|████████████████████████████▋ | ETA: 0:06:21 Progress: 70%|████████████████████████████▊ | ETA: 0:06:16 ====================================================================================== 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 99 running 1 of 1 signal (10): User defined signal 1 jl_gc_wb at /source/src/gc-wb-stock.h:17 [inlined] jl_table_assign_bp at /source/src/iddict.c:84 [inlined] ijl_eqtable_put at /source/src/iddict.c:146 setindex! at ./iddict.jl:86 [inlined] deepcopy_internal at ./deepcopy.jl:132 unknown function (ip: 0x70c6141f0a36) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _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: 0x70c5ead1e706) 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 /opt/julia/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: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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x70c614106a92) 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:2271 [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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_68568.1 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:2271 [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_39417.1 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:2271 [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: 0x70c61d587249) 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: 71%|████████████████████████████▉ | ETA: 0:06:10 ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Progress: 71%|█████████████████████████████▏ | ETA: 0:06:05 ====================================================================================== 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:1217 wait_forever at ./task.jl:1139 jfptr_wait_forever_55536.1 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:2271 [inlined] start_task at /source/src/task.c:1281 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 0x00007ab6990e04c0 Total snapshots: 371. Utilization: 0% ╎371 @Base/task.jl:1139 wait_forever() 370╎ 371 @Base/task.jl:1217 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000070c6035fc010 Total snapshots: 613. Utilization: 100% ╎612 @Base/client.jl:577 _start() ╎ 612 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 612 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 612 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 612 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 612 @Base/loading.jl:3014 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 612 @Base/loading.jl:2954 include_string(mapexpr::typeof(identity), m… ╎ ╎ 612 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 612 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 612 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 612 @Base/loading.jl:3014 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 612 @Base/loading.jl:2954 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 612 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 612 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 612 @Test/src/Test.jl:1952 macro expansion ╎ ╎ ╎ 612 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 612 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 87 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:0 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 12 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 12 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:123 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 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 @VCFTools/…ts.jl:125 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 8 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 5 @Base/…ators.jl:424 > 5╎ ╎ ╎ ╎ ╎ 5 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 1 @VCFTools/…t.jl:225 geno_ismissing 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex 1╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 66 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 65 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ 64 @Base/array.jl:2449 findnext 5╎ ╎ ╎ ╎ ╎ 5 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 59 @Base/…ators.jl:1202 Fix ╎ ╎ ╎ ╎ ╎ 59 @Base/…tors.jl:1202 #_#59 ╎ ╎ ╎ ╎ ╎ 59 @Base/…tors.jl:178 isequal 59╎ ╎ ╎ ╎ ╎ 59 @Base/…ring.jl:187 == ╎ ╎ ╎ ╎ 1 @Base/array.jl:2450 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 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 ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:225 geno_ismissing 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:82 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:381 checkbounds ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:83 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:85 aim_select(record::VariantCallFo… 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:45 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:483 next! ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:484 #next!#15 ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:470 lock_if_threading ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:486 #17 ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:211 updateProgress! ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:213 #updateProgress!#9 ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:217 _updateProgress! ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:289 _updateProgress!(p::Progr… ╎ ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:617 printover(io::Base.PipeE… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…/io.jl:239 print ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…io.jl:237 write ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:1150 unsafe_write(s::Base.Pip… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:1065 uv_write(s::Base.PipeEn… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:1110 uv_write_async(s::Base… ╎ ╎ ╎ ╎ 524 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 524 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 109 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 109 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 109 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:147 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:42 ensure_margin! 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:88 * ╎ ╎ ╎ ╎ ╎ 85 @VariantCallFormat/…:165 _read!(reader::VariantCa… 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 macro expansion ╎ ╎ ╎ ╎ ╎ 76 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 44 @Base/array.jl:436 getindex 44╎ ╎ ╎ ╎ ╎ 44 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 29 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 29 @Base/…ray.jl:1348 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1201 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + 8╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ray.jl:1205 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 16 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 16 @Base/…ay.jl:1101 array_new_memory 16╎ ╎ ╎ ╎ ╎ ╎ 16 @Base/…ot.jl:588 GenericMemory 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1190 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:5 Colon ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:417 UnitRange 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:428 unitrange_last ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:215 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:49 resize_and_copy! ╎ ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:55 resize_and_copy! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1540 resize!(a::Vector{UInt8}, … ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1204 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:502 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:56 getindex ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:49 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= 4╎ ╎ ╎ ╎ ╎ 6 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:491 all ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:486 reduce ╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:1050 reduce_and 2╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…cs.jl:1065 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:583 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:56 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:49 checkbounds ╎ ╎ ╎ ╎ ╎ 22 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 22 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 22 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 22 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/io.jl:1167 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:681 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:56 buffermem ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:52 buffersize 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @CodecZlib/…:195 process(codec::GzipDec… 6╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/io.jl:1168 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:298 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:206 eof ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:52 buffersize 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:209 eof ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:302 peek ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:964 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:381 checkbounds 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:965 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1170 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ors.jl:424 > 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/io.jl:1174 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ray.jl:400 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ay.jl:1020 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1024 _setindex! 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 415 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 415 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:385 copy ╎ ╎ ╎ ╎ ╎ 1 @Base/…emory.jl:118 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ 1 @Base/cmem.jl:28 memmove ╎ ╎ ╎ ╎ ╎ 414 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 414 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 414 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 4╎ ╎ ╎ ╎ ╎ 414 @Base/…copy.jl:104 deepcopy_internal ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:588 GenericMemory 43╎ ╎ ╎ ╎ ╎ 43 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 23╎ ╎ ╎ ╎ ╎ 23 @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… 19╎ ╎ ╎ ╎ ╎ 279 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…opy.jl:0 deepcopy_internal(x::Vector{U… ╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ct.jl:182 in 28╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:93 get ╎ ╎ ╎ ╎ ╎ ╎ 31 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:661 Array 2╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ot.jl:649 Array 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:594 memoryref ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ict.jl:81 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:580 >> 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:573 >> 26╎ ╎ ╎ ╎ ╎ ╎ 26 @Base/…ict.jl:86 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ 197 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ct.jl:182 in 62╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 130 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:182 in 30╎ ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:92 get 8╎ ╎ ╎ ╎ ╎ ╎ 100 @Base/…py.jl:104 deepcopy_internal 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…py.jl:108 _deepcopy_memory_t(x::Mem… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ls.jl:868 isbitstype 16╎ ╎ ╎ ╎ ╎ ╎ 81 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:0 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:168 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ry.jl:172 copy(a::Memory{UnitRange… 10╎ ╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ry.jl:173 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ry.jl:136 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ry.jl:118 unsafe_copyto! 6╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…em.jl:28 memmove 44╎ ╎ ╎ ╎ ╎ ╎ 45 @Base/…ct.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:87 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! 37╎ ╎ ╎ ╎ ╎ 37 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 16╎ ╎ ╎ ╎ ╎ 16 @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 @Base/…ion.jl:637 == [99] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 _deepcopy_memory_t at ./deepcopy.jl:123 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: 0x70c5ead1e706) 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 /opt/julia/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: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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x70c614106a92) 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:2271 [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:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_68568.1 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:2271 [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_39417.1 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:2271 [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: 0x70c61d587249) 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: 16109041472 (Pool: 16109025953; Big: 15519); GC: 20052 PkgEval terminated after 2725.92s: test duration exceeded the time limit