Package evaluation to test VCFTools on Julia 1.14.0-DEV.1475 (42ad41c179*) started at 2026-01-11T13:02:22.911 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.35s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.6 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [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 v0.11.37 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [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 5.01s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 12.97s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_w7c1uF/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.9 [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_w7c1uF/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.6 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [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 v0.11.37 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [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 2.8s Test Summary: | Pass Total Time openvcf | 4 4 2.5s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 1.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.3s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:22:45 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 11.135089 seconds (9.82 M allocations: 559.341 MiB, 6.58% gc time, 91.46% compilation time: 17% of which was recompilation) 0.366809 seconds (2.37 M allocations: 141.370 MiB, 7.36% gc time, 14.75% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:20:12 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.183555 seconds (4.02 M allocations: 238.786 MiB, 2.46% gc time, 81.99% compilation time) 0.411460 seconds (2.37 M allocations: 141.365 MiB, 5.73% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 17.1s 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 1.1s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.4s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.7s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.5s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:07 Progress: 0%|▏ | ETA: 0:23:03 Progress: 0%|▏ | ETA: 0:20:38 Progress: 0%|▏ | ETA: 0:21:47 Progress: 0%|▎ | ETA: 0:20:34 Progress: 1%|▎ | ETA: 0:19:55 Progress: 1%|▎ | ETA: 0:20:34 Progress: 1%|▍ | ETA: 0:20:07 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ETA: 21:35:41 Progress: 11%|████▍ | ETA: 0:16:07 Progress: 31%|████████████▋ | ETA: 0:04:21 Progress: 51%|████████████████████▉ | ETA: 0:01:54 Progress: 71%|█████████████████████████████▏ | ETA: 0:00:49 Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:12 Progress: 100%|█████████████████████████████████████████| Time: 0:02:00 [ Info: 823 records are matched 245.649929 seconds (2.01 G allocations: 106.140 GiB, 17.38% gc time, 0.39% compilation time: 9% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:25:24 Progress: 0%|▏ | ETA: 0:20:47 Progress: 0%|▏ | ETA: 0:19:50 Progress: 0%|▏ | ETA: 0:21:31 Progress: 0%|▎ | ETA: 0:20:37 Progress: 1%|▎ | ETA: 0:19:55 Progress: 1%|▎ | ETA: 0:20:34 Progress: 1%|▍ | ETA: 0:20:01 Progress: 1%|▍ | ETA: 0:19:32 Progress: 1%|▍ | ETA: 0:19:57 Progress: 1%|▌ | ETA: 0:19:21 Progress: 1%|▌ | ETA: 0:19:06 Progress: 1%|▌ | ETA: 0:19:28 Progress: 1%|▋ | ETA: 0:19:13 Progress: 2%|▋ | ETA: 0:19:04 Progress: 2%|▋ | 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27%|███████████▎ | ETA: 0:05:32 Progress: 45%|██████████████████▍ | ETA: 0:02:35 Progress: 62%|█████████████████████████▌ | ETA: 0:01:17 Progress: 81%|█████████████████████████████████▎ | ETA: 0:00:30 Progress: 100%|█████████████████████████████████████████| Time: 0:02:09 [ Info: 488 records are matched 260.396766 seconds (2.01 G allocations: 106.121 GiB, 17.90% gc time, 0.23% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:34:06 Progress: 0%|▏ | ETA: 0:25:35 Progress: 0%|▏ | ETA: 0:23:07 Progress: 0%|▏ | ETA: 0:24:42 Progress: 0%|▏ | ETA: 0:23:18 Progress: 1%|▎ | ETA: 0:21:56 Progress: 1%|▎ | ETA: 0:22:33 Progress: 1%|▎ | ETA: 0:21:49 Progress: 1%|▍ | ETA: 0:21:17 Progress: 1%|▍ | ETA: 0:20:53 Progress: 1%|▍ | ETA: 0:21:26 Progress: 1%|▌ | ETA: 0:21:09 Progress: 1%|▌ | ETA: 0:20:55 Progress: 1%|▌ | ETA: 0:20:38 Progress: 1%|▋ | ETA: 0:21:03 Progress: 1%|▋ | ETA: 0:20:51 Progress: 2%|▋ | ETA: 0:20:35 Progress: 2%|▊ | ETA: 0:20:56 Progress: 2%|▊ | ETA: 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10%|████▏ | ETA: 0:19:44 Progress: 10%|████▏ | ETA: 0:19:41 Progress: 10%|████▎ | ETA: 0:19:39 Progress: 100%|█████████████████████████████████████████| Time: 0:02:15 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 1 days, 1:02:22 Progress: 8%|███▏ | ETA: 0:27:30 Progress: 27%|███████████ | ETA: 0:06:08 Progress: 47%|███████████████████▌ | ETA: 0:02:31 Progress: 67%|███████████████████████████▍ | ETA: 0:01:08 Progress: 89%|████████████████████████████████████▍ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:02:19 [ Info: 0 records are matched 285.680484 seconds (2.01 G allocations: 106.121 GiB, 18.42% gc time, 0.22% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 13m19.4s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 23:20:07 Progress: 14%|█████▊ | ETA: 0:12:41 Progress: 33%|█████████████▍ | ETA: 0:04:22 Progress: 51%|████████████████████▉ | ETA: 0:02:04 Progress: 69%|████████████████████████████▎ | ETA: 0:00:58 Progress: 89%|████████████████████████████████████▍ | ETA: 0:00:16 Progress: 100%|█████████████████████████████████████████| Time: 0:02:11 [ Info: 833 records are matched 141.220115 seconds (1.02 G allocations: 53.885 GiB, 15.86% gc time, 0.30% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 0:48:58 Progress: 17%|██████▉ | ETA: 0:11:00 Progress: 36%|██████████████▋ | ETA: 0:04:03 Progress: 56%|██████████████████████▉ | ETA: 0:01:47 Progress: 76%|███████████████████████████████▏ | ETA: 0:00:43 Progress: 99%|████████████████████████████████████████▉| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:02:18 [ Info: 493 records are matched 148.050339 seconds (1.02 G allocations: 53.885 GiB, 15.85% gc time, 0.29% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:44:31 Progress: 20%|████████▏ | ETA: 0:07:51 Progress: 39%|████████████████ | ETA: 0:03:05 Progress: 63%|██████████████████████████ | ETA: 0:01:09 Progress: 86%|███████████████████████████████████▎ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 0 records are matched 131.092896 seconds (1.02 G allocations: 53.885 GiB, 15.02% gc time, 0.31% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 7m02.8s 0.888950 seconds (1.26 M allocations: 68.081 MiB, 2.17% gc time, 81.26% compilation time) 0.743240 seconds (1.16 M allocations: 64.747 MiB, 80.14% compilation time) 0.779572 seconds (1.16 M allocations: 63.787 MiB, 3.14% gc time, 82.29% compilation time) 0.326238 seconds (207.71 k allocations: 10.888 MiB, 99.96% compilation time) 0.011686 seconds (6.46 k allocations: 398.680 KiB, 97.44% compilation time) 0.007541 seconds (2.65 k allocations: 165.445 KiB, 96.58% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 6.5s 1.091418 seconds (1.04 M allocations: 58.270 MiB, 41.51% gc time, 46.06% compilation time) 0.577711 seconds (884.43 k allocations: 52.066 MiB, 75.34% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 4.4s Test Summary: | Pass Total Time convert_ds | 5 5 0.8s 0.124919 seconds (525.74 k allocations: 30.690 MiB, 28.59% gc time, 23.26% compilation time) 0.435622 seconds (647.59 k allocations: 37.464 MiB, 87.44% 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 0.048309 seconds (520.58 k allocations: 32.160 MiB) 0.317882 seconds (597.97 k allocations: 36.534 MiB, 4.55% gc time, 79.62% 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 0.513578 seconds (1.56 M allocations: 62.080 MiB, 81.60% gc time, 1.31% compilation time) 0.405678 seconds (1.71 M allocations: 70.413 MiB, 77.98% 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 4.3s Test Summary: | Pass Total Time record info | 14 14 2.8s Test Summary: | Pass Total Time write VCF | 3 3 2.2s 1.658833 seconds (4.80 M allocations: 296.616 MiB, 4.39% gc time, 44.89% compilation time) 1.100913 seconds (2.39 M allocations: 142.854 MiB, 4.47% gc time, 15.87% compilation time) 0.915764 seconds (4.42 M allocations: 276.395 MiB, 6.13% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 5.8s 0.980075 seconds (606.37 k allocations: 33.463 MiB, 2.14% gc time, 31.53% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 2.9s Test Summary: | Pass Total Time filter_chr | 4 4 2.1s Progress: 0%|▏ | ETA: 0:26:13 Progress: 1%|▎ | ETA: 0:26:19 Progress: 1%|▍ | ETA: 0:24:55 Progress: 1%|▌ | ETA: 0:25:07 Progress: 2%|▊ | ETA: 0:24:27 Progress: 2%|▉ | ETA: 0:24:35 Progress: 2%|█ | ETA: 0:24:03 Progress: 3%|█▏ | ETA: 0:24:07 Progress: 3%|█▍ | ETA: 0:23:35 Progress: 4%|█▌ | ETA: 0:23:35 Progress: 4%|█▋ | ETA: 0:23:40 Progress: 4%|█▊ | ETA: 0:23:32 Progress: 5%|█▉ | ETA: 0:23:39 Progress: 5%|██▏ | ETA: 0:23:23 Progress: 5%|██▎ | ETA: 0:23:24 Progress: 6%|██▍ | ETA: 0:23:10 Progress: 6%|██▌ | ETA: 0:23:10 Progress: 7%|██▋ | ETA: 0:23:01 Progress: 7%|██▉ | ETA: 0:23:02 Progress: 7%|███ | ETA: 0:22:55 Progress: 8%|███▏ | ETA: 0:22:52 Progress: 8%|███▎ | ETA: 0:22:49 Progress: 8%|███▍ | ETA: 0:22:32 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Progress: 89%|████████████████████████████████████▍ | ETA: 0:02:44 ====================================================================================== 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 9 running 1 of 1 signal (10): User defined signal 1 ijl_unbox_int64 at /source/src/datatype.c:1489 jl_f_memoryrefnew at /source/src/builtins.c:1817 _deepcopy_memory_t at ./deepcopy.jl:116 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x78df4414bfd6) 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:1995 [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:746 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x78df65912662) 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:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:757 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_42437.1 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:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:757 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_44588.1 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:2285 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x78df6717c249) 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: 89%|████████████████████████████████████▌ | ETA: 0:02:39┌ 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 0x000078df4cbfc010 Total snapshots: 657. Utilization: 100% ╎655 @Base/client.jl:585 _start() ╎ 655 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 655 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 655 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 655 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 655 @Base/loading.jl:3211 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 655 @Base/loading.jl:3151 include_string(mapexpr::typeof(identity), m… ╎ ╎ 655 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 655 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 655 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 655 @Base/loading.jl:3211 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 655 @Base/loading.jl:3151 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 655 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 655 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 655 @Test/src/Test.jl:1995 macro expansion ╎ ╎ ╎ 655 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 655 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 80 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 7 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 7 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 4 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:424 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 3 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:964 getindex ╎ ╎ ╎ ╎ ╎ 3 @Base/…ials.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ 3 @Base/…ials.jl:381 checkbounds ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:11 length 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:10 size 1╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:3197 getindex 1╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:943 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 68 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 66 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ 66 @Base/array.jl:2449 findnext 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 64 @Base/…ators.jl:1203 Fix ╎ ╎ ╎ ╎ ╎ 64 @Base/…tors.jl:1203 #_#59 ╎ ╎ ╎ ╎ ╎ 64 @Base/…tors.jl:178 isequal 64╎ ╎ ╎ ╎ ╎ 64 @Base/…ring.jl:187 == 2╎ ╎ ╎ ╎ 2 @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 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:673 isequaldata 2╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:78 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╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:217 _updateProgress! ╎ ╎ ╎ ╎ 574 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 574 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 84 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 84 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 84 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 70 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 62 @Automa/…en.jl:449 macro expansion 1╎ ╎ ╎ ╎ ╎ 1 @Base/…iler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ 18 @Base/array.jl:436 getindex 18╎ ╎ ╎ ╎ ╎ 18 @Base/boot.jl:676 Array ╎ ╎ ╎ ╎ ╎ 43 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 42 @Base/…ray.jl:1348 _push! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1197 _growend! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ler.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1202 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1204 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 4╎ ╎ ╎ ╎ ╎ ╎ 38 @Base/…ray.jl:1205 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1158 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ay.jl:1101 array_new_memory 24╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ot.jl:615 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:1184 _growend_internal!(a::Vect… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ot.jl:622 memoryref 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1190 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1349 _push! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…iler.jl:0 __safe_setindex! ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:572 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…yops.jl:51 vload ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…sics.jl:477 load 1╎ ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…ics.jl:486 macro expansion 1╎ ╎ ╎ ╎ ╎ 4 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…dvec.jl:491 all ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…dvec.jl:486 reduce ╎ ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…ics.jl:1050 reduce_and 3╎ ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…cs.jl:1065 macro expansion 1╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:584 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:1454 in 2╎ ╎ ╎ ╎ ╎ 2 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 14 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 14 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 14 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 14 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/io.jl:1167 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 5 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:623 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:746 readdata!(inpu… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:906 unsafe_read ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:44 unsafe_read(s::IOStrea… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ck.jl:272 unlock 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ck.jl:278 (::Base.var"#_unloc… ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @CodecZlib/…:195 process(codec::GzipDec… 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/io.jl:1168 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:298 peek 4╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:209 eof ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:302 peek ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ls.jl:964 getindex 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ls.jl:385 checkbounds ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:307 read ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:97 consumed! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:98 #consumed!#1 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1174 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:393 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1020 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 490 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 490 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 490 @Base/…epcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 490 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 490 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 6╎ ╎ ╎ ╎ ╎ 490 @Base/…copy.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:0 _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 6 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:615 GenericMemory 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:115 _deepcopy_memory_t(x::Memor… 60╎ ╎ ╎ ╎ ╎ 60 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 8╎ ╎ ╎ ╎ ╎ 8 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 7╎ ╎ ╎ ╎ ╎ 7 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 3╎ ╎ ╎ ╎ ╎ 3 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 17╎ ╎ ╎ ╎ ╎ 340 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:182 in 20╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 61 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/boot.jl:688 Array 9╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ot.jl:676 Array ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ict.jl:81 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 50╎ ╎ ╎ ╎ ╎ ╎ 50 @Base/…ict.jl:86 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ict.jl:87 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…lue.jl:59 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 4╎ ╎ ╎ ╎ ╎ ╎ 239 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ct.jl:182 in 64╎ ╎ ╎ ╎ ╎ ╎ 64 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 169 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 26 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 26 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 26 @Base/…ct.jl:182 in 26╎ ╎ ╎ ╎ ╎ ╎ ╎ 26 @Base/…ct.jl:92 get 9╎ ╎ ╎ ╎ ╎ ╎ 143 @Base/…py.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 13╎ ╎ ╎ ╎ ╎ ╎ 131 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:189 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ry.jl:193 copy(a::Memory{UnitRange… 28╎ ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ot.jl:615 GenericMemory 1╎ ╎ ╎ ╎ ╎ ╎ 24 @Base/…ry.jl:194 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ry.jl:157 unsafe_copyto! 12╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ot.jl:622 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ry.jl:139 unsafe_copyto! 11╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…em.jl:28 memmove 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:81 setindex! 55╎ ╎ ╎ ╎ ╎ ╎ 56 @Base/…ct.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ct.jl:87 setindex! 7╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…er.jl:61 setproperty! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 44╎ ╎ ╎ ╎ ╎ 44 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 13╎ ╎ ╎ ╎ ╎ 13 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:125 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nge.jl:925 iterate 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ion.jl:637 == ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1246 wait_forever at ./task.jl:1168 jfptr_wait_forever_79418.1 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:2285 [inlined] start_task at /source/src/task.c:1272 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Progress: 90%|█████████████████████████████████████ | ETA: 0:02:23┌ 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 0x0000730537ca7b20 Total snapshots: 368. Utilization: 0% ╎368 @Base/task.jl:1168 wait_forever() 367╎ 368 @Base/task.jl:1246 wait() Progress: 91%|█████████████████████████████████████▏ | ETA: 0:02:17 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 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_79418.1 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:2285 [inlined] start_task at /source/src/task.c:1272 unknown function (ip: (nil)) at (unknown file) Allocations: 19803745 (Pool: 19803089; Big: 656); GC: 13 [9] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 get at ./iddict.jl:92 [inlined] in at ./iddict.jl:182 [inlined] haskey at ./abstractdict.jl:19 [inlined] deepcopy_internal at ./deepcopy.jl:138 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x78df6599c2f6) 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/tQ143/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x78df4414bfd6) 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:1995 [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:746 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 unknown function (ip: 0x78df65912662) 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:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:757 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 include_string at ./loading.jl:3151 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3211 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_42437.1 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:2285 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:757 jl_eval_toplevel_stmts at /source/src/toplevel.c:600 jl_toplevel_eval_flex at /source/src/toplevel.c:698 ijl_toplevel_eval at /source/src/toplevel.c:769 ijl_toplevel_eval_in at /source/src/toplevel.c:814 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_44588.1 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:2285 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x78df6717c249) 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: 17953628762 (Pool: 17953613294; Big: 15468); GC: 18345 PkgEval terminated after 2732.02s: test duration exceeded the time limit