Package evaluation of VCFTools on Julia 1.13.0-DEV.971 (04e26c5eae*) started at 2025-08-10T17:57:33.394 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.67s ################################################################################ # 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 v0.8.4 [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 v0.19.0 [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 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.8 [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 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [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 [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 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.59s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 36.57s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_hxvxcS/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 ⌃ [a93c6f00] DataFrames v1.5.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.10.4 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.6 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [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_hxvxcS/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 ⌅ [67c07d97] Automa v0.8.4 [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 v1.5.0 [864edb3b] DataStructures v0.19.0 [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 v1.4.4 [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 v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.8 [91c51154] SentinelArrays v1.4.8 [66db9d55] SnoopPrecompile v1.0.3 [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 v0.9.13 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [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 v8.15.0+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+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 v1.65.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling packages... 38162.4 ms ✓ CSV 1 dependency successfully precompiled in 39 seconds. 38 already precompiled. Precompiling packages... 31757.1 ms ✓ PrettyTables 79085.3 ms ✓ DataFrames 2 dependencies successfully precompiled in 111 seconds. 35 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 3.6s Test Summary: | Pass Total Time openvcf | 4 4 2.4s 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 2.4s ┌ 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: 0:25:10 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 14.470985 seconds (10.60 M allocations: 664.728 MiB, 4.92% gc time, 95.87% compilation time: 21% of which was recompilation) 0.490771 seconds (2.86 M allocations: 195.913 MiB, 8.70% gc time, 18.45% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:23:14 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.483579 seconds (4.37 M allocations: 297.767 MiB, 3.00% gc time, 82.90% compilation time) 0.432778 seconds (2.85 M allocations: 195.284 MiB, 6.69% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.7s Test Summary: | Pass Total Time get sampleID | 4 4 0.0s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.8s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.2s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 5.9s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:15 Progress: 0%|▏ | ETA: 0:19:55 Progress: 0%|▏ | ETA: 0:19:49 Progress: 0%|▏ | ETA: 0:19:39 Progress: 0%|▏ | ETA: 0:19:47 Progress: 1%|▎ | ETA: 0:19:39 Progress: 1%|▎ | ETA: 0:19:32 Progress: 1%|▎ | ETA: 0:19:27 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Time: 0:01:59 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 22:26:43 Progress: 18%|███████▎ | ETA: 0:09:17 Progress: 35%|██████████████▌ | ETA: 0:03:42 Progress: 55%|██████████████████████▍ | ETA: 0:01:42 Progress: 74%|██████████████████████████████▎ | ETA: 0:00:44 Progress: 95%|██████████████████████████████████████▊ | ETA: 0:00:07 Progress: 100%|█████████████████████████████████████████| Time: 0:02:04 [ Info: 488 records are matched 255.051402 seconds (2.19 G allocations: 143.726 GiB, 6.69% gc time, 0.32% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:21:41 Progress: 0%|▏ | ETA: 0:20:49 Progress: 0%|▏ | ETA: 0:20:26 Progress: 0%|▏ | ETA: 0:20:11 Progress: 0%|▏ | ETA: 0:20:03 Progress: 0%|▎ | ETA: 0:20:00 Progress: 1%|▎ | ETA: 0:19:54 Progress: 1%|▎ | ETA: 0:19:54 Progress: 1%|▎ | ETA: 0:19:53 Progress: 1%|▍ | ETA: 0:19:49 Progress: 1%|▍ | ETA: 0:19:46 Progress: 1%|▍ | ETA: 0:19:44 Progress: 1%|▌ | ETA: 0:19:40 Progress: 1%|▌ | ETA: 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| ETA: 0:17:47 Progress: 9%|███▉ | ETA: 0:17:46 Progress: 10%|███▉ | ETA: 0:17:45 Progress: 10%|███▉ | ETA: 0:17:44 Progress: 10%|████ | ETA: 0:17:43 Progress: 10%|████ | ETA: 0:17:43 Progress: 10%|████ | ETA: 0:17:42 Progress: 10%|████▏ | ETA: 0:17:41 Progress: 10%|████▏ | ETA: 0:17:40 Progress: 10%|████▏ | ETA: 0:17:39 Progress: 10%|████▏ | ETA: 0:17:38 Progress: 10%|████▎ | ETA: 0:17:37 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 22:19:35 Progress: 18%|███████▎ | ETA: 0:09:20 Progress: 36%|██████████████▋ | ETA: 0:03:39 Progress: 55%|██████████████████████▊ | ETA: 0:01:38 Progress: 75%|██████████████████████████████▊ | ETA: 0:00:41 Progress: 96%|███████████████████████████████████████▌ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:02:04 [ Info: 0 records are matched 256.798296 seconds (2.19 G allocations: 143.725 GiB, 6.69% gc time, 0.35% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m50.1s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:56:03 Progress: 17%|███████ | ETA: 0:09:27 Progress: 36%|██████████████▋ | ETA: 0:03:35 Progress: 55%|██████████████████████▊ | ETA: 0:01:36 Progress: 75%|██████████████████████████████▉ | ETA: 0:00:40 Progress: 97%|███████████████████████████████████████▋ | ETA: 0:00:04 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 833 records are matched 132.775812 seconds (1.11 G allocations: 72.816 GiB, 6.49% gc time, 0.43% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:06:15 Progress: 19%|███████▋ | ETA: 0:08:39 Progress: 38%|███████████████▍ | ETA: 0:03:19 Progress: 58%|███████████████████████▋ | ETA: 0:01:28 Progress: 78%|███████████████████████████████▉ | ETA: 0:00:35 Progress: 99%|████████████████████████████████████████▋| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: 493 records are matched 133.274407 seconds (1.11 G allocations: 72.816 GiB, 6.45% gc time, 0.43% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:46:54 Progress: 19%|███████▋ | ETA: 0:08:27 Progress: 38%|███████████████▋ | ETA: 0:03:12 Progress: 59%|████████████████████████▎ | ETA: 0:01:22 Progress: 80%|████████████████████████████████▊ | ETA: 0:00:30 Progress: 100%|█████████████████████████████████████████| Time: 0:02:00 [ Info: 0 records are matched 131.496878 seconds (1.11 G allocations: 72.816 GiB, 5.77% gc time, 0.44% compilation time: <1% of which was recompilation) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m40.1s 1.080444 seconds (1.28 M allocations: 91.384 MiB, 1.60% gc time, 87.94% compilation time) 0.907802 seconds (1.16 M allocations: 86.631 MiB, 2.23% gc time, 85.28% compilation time) 0.901441 seconds (1.16 M allocations: 85.887 MiB, 2.34% gc time, 85.59% compilation time) 0.418151 seconds (203.62 k allocations: 11.567 MiB, 99.96% compilation time) 0.010425 seconds (6.18 k allocations: 483.492 KiB, 95.30% compilation time) 0.009414 seconds (2.65 k allocations: 247.555 KiB, 96.15% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.2s 0.923596 seconds (953.02 k allocations: 74.537 MiB, 2.72% gc time, 83.95% compilation time) 0.801598 seconds (860.77 k allocations: 71.559 MiB, 2.13% gc time, 82.64% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.1s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.126872 seconds (525.31 k allocations: 50.449 MiB, 10.73% gc time, 27.37% compilation time) 0.693519 seconds (647.61 k allocations: 57.718 MiB, 1.64% gc time, 86.49% 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 0.084618 seconds (520.43 k allocations: 51.916 MiB, 11.18% gc time) 0.541351 seconds (589.76 k allocations: 56.017 MiB, 1.97% gc time, 83.75% 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 0.543398 seconds (1.56 M allocations: 81.839 MiB, 73.94% gc time, 1.70% compilation time) 0.622408 seconds (1.70 M allocations: 90.371 MiB, 75.72% 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 7.0s Test Summary: | Pass Total Time record info | 14 14 5.0s Test Summary: | Pass Total Time write VCF | 3 3 4.4s 2.771903 seconds (5.28 M allocations: 380.199 MiB, 2.73% gc time, 44.97% compilation time) 1.252506 seconds (2.86 M allocations: 194.795 MiB, 3.16% gc time, 17.48% compilation time) 0.982666 seconds (4.89 M allocations: 358.313 MiB, 5.97% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.6s 0.990628 seconds (618.95 k allocations: 54.420 MiB, 1.28% gc time, 48.64% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.8s Test Summary: | Pass Total Time filter_chr | 4 4 1.6s Progress: 0%|▏ | ETA: 0:24:50 Progress: 1%|▎ | ETA: 0:22:59 Progress: 1%|▌ | ETA: 0:22:37 Progress: 1%|▋ | ETA: 0:22:20 Progress: 2%|▊ | ETA: 0:22:08 Progress: 2%|▉ | ETA: 0:22:01 Progress: 3%|█▏ | ETA: 0:21:52 Progress: 3%|█▎ | ETA: 0:21:47 Progress: 3%|█▍ | ETA: 0:21:44 Progress: 4%|█▌ | ETA: 0:21:38 Progress: 4%|█▋ | ETA: 0:21:35 Progress: 4%|█▉ | ETA: 0:21:31 Progress: 5%|██ | ETA: 0:21:28 Progress: 5%|██▏ | ETA: 0:21:23 Progress: 6%|██▎ | ETA: 0:21:18 Progress: 6%|██▌ | ETA: 0:21:10 Progress: 6%|██▋ | ETA: 0:21:05 Progress: 7%|██▊ | ETA: 0:21:01 Progress: 7%|██▉ | ETA: 0:20:57 Progress: 7%|███ | ETA: 0:20:53 Progress: 8%|███▎ | ETA: 0:20:49 Progress: 8%|███▍ | ETA: 0:20:44 Progress: 9%|███▌ | ETA: 0:20:39 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A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 27 running 1 of 1 signal (10): User defined signal 1 immut_id_ at /source/src/builtins.c:415 ijl_object_id_ at /source/src/builtins.c:504 [inlined] jl_table_peek_bp at /source/src/iddict.c:118 [inlined] ijl_eqtable_get at /source/src/iddict.c:157 get at ./iddict.jl:92 [inlined] in at ./iddict.jl:182 [inlined] haskey at ./abstractdict.jl:19 [inlined] deepcopy_internal at ./deepcopy.jl:138 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x7ac580f26ca6) at (unknown file) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 _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/YgfJC/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: 0x7ac56234e616) at (unknown file) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 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:1929 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_invoke at /source/src/gf.c:4022 jl_toplevel_eval_flex at /source/src/toplevel.c:762 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2847 _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 _include at ./loading.jl:2907 include at ./Base.jl:312 IncludeInto at ./Base.jl:313 jfptr_IncludeInto_36308.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2847 _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 _include at ./loading.jl:2907 include at ./Base.jl:312 IncludeInto at ./Base.jl:313 jfptr_IncludeInto_36308.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 exec_options at ./client.jl:286 _start at ./client.jl:553 jfptr__start_70166.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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: 0x7ac582244249) 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 ============================================================== Progress: 87%|███████████████████████████████████▋ | ETA: 0:02:51 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== 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:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_30142.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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 ============================================================== ┌ 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 0x00007b2a61b01960 Total snapshots: 406. Utilization: 0% ╎406 @Base/task.jl:1129 wait_forever() 405╎ 406 @Base/task.jl:1192 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 0x00007ac568000010 Total snapshots: 518. Utilization: 100% ╎515 @Base/client.jl:553 _start() ╎ 515 @Base/client.jl:286 exec_options(opts::Base.JLOptions) ╎ 515 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 515 @Base/Base.jl:313 (::Base.IncludeInto)(fname::String) ╎ 515 @Base/Base.jl:312 include(mapexpr::Function, mod::Module, _path::St… ╎ 515 @Base/loading.jl:2907 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 515 @Base/loading.jl:2847 include_string(mapexpr::typeof(identity), m… ╎ ╎ 515 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 515 @Base/Base.jl:313 (::Base.IncludeInto)(fname::String) ╎ ╎ 515 @Base/Base.jl:312 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 515 @Base/loading.jl:2907 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 515 @Base/loading.jl:2847 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 515 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 515 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 515 @Test/src/Test.jl:1929 macro expansion ╎ ╎ ╎ 515 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 515 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 81 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 11 @VCFTools/…ct.jl:65 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 11 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 8 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 4 @Base/…ators.jl:425 > 4╎ ╎ ╎ ╎ ╎ 4 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 1 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:387 checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:383 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:11 length ╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:3158 getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:954 _getindex 2╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:941 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 63 @VCFTools/…ct.jl:74 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 63 @Base/array.jl:2465 findfirst ╎ ╎ ╎ ╎ 62 @Base/array.jl:2414 findnext 5╎ ╎ ╎ ╎ ╎ 5 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 57 @Base/…ators.jl:1195 Fix ╎ ╎ ╎ ╎ ╎ 57 @Base/…tors.jl:1195 #_#58 ╎ ╎ ╎ ╎ ╎ 57 @Base/…tors.jl:178 isequal 57╎ ╎ ╎ ╎ ╎ 57 @Base/…ring.jl:186 == ╎ ╎ ╎ ╎ 1 @Base/array.jl:2415 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 2 @VCFTools/…ct.jl:76 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 2 @Base/array.jl:2465 findfirst 1╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:2414 findnext ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:673 isequaldata 1╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 1 @VCFTools/…ct.jl:79 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:225 geno_ismissing 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ct.jl:82 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3158 getindex ╎ ╎ ╎ ╎ 1 @Base/range.jl:954 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:941 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:522 <= ╎ ╎ ╎ ╎ 1 @VCFTools/…ct.jl:83 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3158 getindex ╎ ╎ ╎ ╎ 1 @Base/range.jl:954 _getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:941 _in_unit_range ╎ ╎ ╎ ╎ 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╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:114 gtstats(record::VariantCallForma… ╎ ╎ ╎ ╎ 434 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 434 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 64 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 64 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 64 @VariantCallFormat/…:147 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:160 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:2090 empty! ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1253 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:219 _unsetindex! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:596 memoryref ╎ ╎ ╎ ╎ ╎ 54 @VariantCallFormat/…:169 _read!(reader::VariantCa… 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:0 macro expansion ╎ ╎ ╎ ╎ ╎ 49 @Automa/…en.jl:263 macro expansion ╎ ╎ ╎ ╎ ╎ 16 @Base/array.jl:411 getindex 16╎ ╎ ╎ ╎ ╎ 16 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 29 @Base/array.jl:1310 push! ╎ ╎ ╎ ╎ ╎ 28 @Base/…ray.jl:1313 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1175 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:11 length ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1180 _growend! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 25 @Base/…ray.jl:1181 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:0 _growend_internal!(a::Vector{… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1134 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1140 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ay.jl:1156 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ay.jl:1076 array_new_memory 10╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1159 _growend_internal!(a::Vect… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ot.jl:595 memoryref 9╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ay.jl:1165 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1314 _push! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 __safe_setindex! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:387 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:383 checkbounds 3╎ ╎ ╎ ╎ ╎ 3 @Base/…ials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:291 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Automa/…ry.jl:56 getindex 1╎ ╎ ╎ ╎ ╎ 2 @Automa/…ry.jl:49 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:522 <= ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:57 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…nter.jl:151 unsafe_load ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:292 macro expansion ╎ ╎ ╎ ╎ ╎ 7 @VariantCallFormat/…:185 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 7 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 7 @BufferedStreams/…:71 fillbuffer! ╎ ╎ ╎ ╎ ╎ 7 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:387 readbytes!(stream::… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:201 eof(stream::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:582 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:595 fillbuffer(strea… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:696 readdata!(input… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:899 unsafe_read 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:43 unsafe_read(s::IOStream… ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:596 fillbuffer(strea… ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:656 callprocess(str… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @CodecZlib/…:195 process(codec::GzipDeco… 6╎ ╎ ╎ ╎ ╎ ╎ ╎ 6 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ 370 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 370 @VariantCallFormat/…:309 copy(record::VariantCallFo… 1╎ ╎ ╎ ╎ ╎ 370 @Base/…epcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 369 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 369 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 3╎ ╎ ╎ ╎ ╎ 369 @Base/…copy.jl:104 deepcopy_internal ╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:594 memoryref 50╎ ╎ ╎ ╎ ╎ 50 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 7╎ ╎ ╎ ╎ ╎ 7 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 3╎ ╎ ╎ ╎ ╎ 3 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 20╎ ╎ ╎ ╎ ╎ 262 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ct.jl:182 in 32╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 38 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:661 Array 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ot.jl:649 Array ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ict.jl:85 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…lue.jl:8 RefValue 33╎ ╎ ╎ ╎ ╎ ╎ 33 @Base/…ict.jl:86 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ict.jl:87 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…lue.jl:59 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 3╎ ╎ ╎ ╎ ╎ ╎ 170 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 45 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 45 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 45 @Base/…ct.jl:182 in 45╎ ╎ ╎ ╎ ╎ ╎ 45 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 118 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ct.jl:182 in 23╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @Base/…ct.jl:92 get 6╎ ╎ ╎ ╎ ╎ ╎ 95 @Base/…py.jl:104 deepcopy_internal 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @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 22╎ ╎ ╎ ╎ ╎ ╎ 84 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:175 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ry.jl:179 copy(a::Memory{UnitRange… 11╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ry.jl:180 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ry.jl:143 unsafe_copyto! 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ry.jl:125 unsafe_copyto! 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:85 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ue.jl:8 RefValue 42╎ ╎ ╎ ╎ ╎ ╎ 42 @Base/…ct.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 29╎ ╎ ╎ ╎ ╎ 29 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 12╎ ╎ ╎ ╎ ╎ 12 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… [27] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 copy at ./array.jl:0 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/YgfJC/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: 0x7ac56234e616) at (unknown file) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 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:1929 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_invoke at /source/src/gf.c:4022 jl_toplevel_eval_flex at /source/src/toplevel.c:762 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2847 _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 _include at ./loading.jl:2907 include at ./Base.jl:312 IncludeInto at ./Base.jl:313 jfptr_IncludeInto_36308.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2847 _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 _include at ./loading.jl:2907 include at ./Base.jl:312 IncludeInto at ./Base.jl:313 jfptr_IncludeInto_36308.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 exec_options at ./client.jl:286 _start at ./client.jl:553 jfptr__start_70166.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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: 0x7ac582244249) 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: 19231547551 (Pool: 19231531965; Big: 15586); GC: 35116 PkgEval terminated after 2728.61s: test duration exceeded the time limit