Package evaluation of VCFTools on Julia 1.13.0-DEV.820 (69a2a571e8*) started at 2025-07-08T18:41:36.008 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.62s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed MacroTools ────────────── v0.5.16 Installed CommonSolve ───────────── v0.2.4 Installed DelimitedFiles ────────── v1.9.1 Installed FillArrays ────────────── v1.13.0 Installed DataStructures ────────── v0.18.22 Installed AliasTables ───────────── v1.1.3 Installed OrderedCollections ────── v1.8.1 Installed HypergeometricFunctions ─ v0.3.28 Installed CodecZlib ─────────────── v0.7.8 Installed ConstructionBase ──────── v1.6.0 Installed TranscodingStreams ────── v0.9.13 Installed StatsBase ─────────────── v0.34.5 Installed VCFTools ──────────────── v0.2.10 Installed Combinatorics ─────────── v1.0.3 Installed Compat ────────────────── v4.17.0 Installed StatsAPI ──────────────── v1.7.1 Installed DataAPI ───────────────── v1.16.0 Installed ProgressMeter ─────────── v1.10.4 Installed IrrationalConstants ───── v0.2.4 Installed Statistics ────────────── v1.11.1 Installed Rmath ─────────────────── v0.8.0 Installed BufferedStreams ───────── v1.2.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed QuadGK ────────────────── v2.11.2 Installed LogExpFunctions ───────── v0.3.29 Installed Roots ─────────────────── v2.2.8 Installed HypothesisTests ───────── v0.11.5 Installed BioGenerics ───────────── v0.1.5 Installed PtrArrays ─────────────── v1.3.0 Installed StatsFuns ─────────────── v1.5.0 Installed InverseFunctions ──────── v0.1.17 Installed SpecialFunctions ──────── v2.5.1 Installed Reexport ──────────────── v1.2.2 Installed Distributions ─────────── v0.25.120 Installed Preferences ───────────── v1.4.3 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.0 Installed PDMats ────────────────── v0.11.35 Installed SortingAlgorithms ─────── v1.2.1 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.42 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.6 Installed Automa ────────────────── v0.8.4 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 ⌅ [67c07d97] + Automa 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 [34da2185] + Compat v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [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 v1.7.0 [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 [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 v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [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 v1.12.0 [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 v1.12.0 [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 [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 7.42s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4777.4 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 363.08s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_AAcnDq/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [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 v0.34.5 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_AAcnDq/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 v4.17.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [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 v1.7.0 [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 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [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 v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [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 v8.14.1+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [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 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 4.1s 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 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.5s ┌ 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: 0:27:55 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 15.500763 seconds (11.06 M allocations: 677.598 MiB, 4.67% gc time, 93.17% compilation time: 21% of which was recompilation) 0.463965 seconds (2.87 M allocations: 195.737 MiB, 11.61% gc time, 18.77% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:24:38 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.576768 seconds (4.39 M allocations: 297.993 MiB, 3.01% gc time, 84.68% compilation time) 0.409081 seconds (2.85 M allocations: 195.339 MiB, 6.89% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.0s 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 1.9s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.0s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 5.5s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:33 Progress: 0%|▏ | ETA: 0:18:57 Progress: 0%|▏ | ETA: 0:18:51 Progress: 0%|▏ | ETA: 0:18:46 Progress: 0%|▏ | ETA: 0:18:30 Progress: 1%|▎ | ETA: 0:18:24 Progress: 1%|▎ | ETA: 0:18:16 Progress: 1%|▎ | ETA: 0:18:10 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ETA: 0:16:02 Progress: 10%|███▉ | ETA: 0:16:02 Progress: 10%|████ | ETA: 0:16:01 Progress: 10%|████ | ETA: 0:16:00 Progress: 10%|████ | ETA: 0:15:59 Progress: 10%|████ | ETA: 0:15:58 Progress: 10%|████▏ | ETA: 0:15:57 Progress: 10%|████▏ | ETA: 0:15:57 Progress: 10%|████▏ | ETA: 0:15:56 Progress: 10%|████▎ | ETA: 0:15:55 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:45:07 Progress: 19%|███████▉ | ETA: 0:07:47 Progress: 38%|███████████████▊ | ETA: 0:03:01 Progress: 60%|████████████████████████▋ | ETA: 0:01:16 Progress: 82%|█████████████████████████████████▌ | ETA: 0:00:26 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 0 records are matched 236.282189 seconds (2.19 G allocations: 143.726 GiB, 6.54% gc time, 0.38% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m52.6s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:45:11 Progress: 19%|███████▋ | ETA: 0:07:45 Progress: 38%|███████████████▋ | ETA: 0:02:54 Progress: 60%|████████████████████████▍ | ETA: 0:01:13 Progress: 81%|█████████████████████████████████▎ | ETA: 0:00:25 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 833 records are matched 120.391786 seconds (1.11 G allocations: 72.817 GiB, 6.47% gc time, 0.53% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:04:18 Progress: 21%|████████▌ | ETA: 0:06:50 Progress: 43%|█████████████████▋ | ETA: 0:02:25 Progress: 65%|██████████████████████████▉ | ETA: 0:00:58 Progress: 89%|████████████████████████████████████▍ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: 493 records are matched 121.733387 seconds (1.11 G allocations: 72.816 GiB, 6.29% gc time, 0.51% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:02:06 Progress: 21%|████████▋ | ETA: 0:06:26 Progress: 43%|█████████████████▌ | ETA: 0:02:19 Progress: 65%|██████████████████████████▊ | ETA: 0:00:56 Progress: 88%|████████████████████████████████████▏ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 0 records are matched 115.488821 seconds (1.11 G allocations: 72.816 GiB, 6.24% gc time, 0.44% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 5m59.9s 1.137503 seconds (1.35 M allocations: 93.346 MiB, 4.22% gc time, 85.67% compilation time) 0.938227 seconds (1.22 M allocations: 88.393 MiB, 3.63% gc time, 80.48% compilation time) 0.890230 seconds (1.22 M allocations: 87.640 MiB, 2.52% gc time, 83.20% compilation time) 0.431748 seconds (220.02 k allocations: 12.054 MiB, 99.96% compilation time) 0.009993 seconds (6.30 k allocations: 484.914 KiB, 96.26% compilation time) 0.009093 seconds (2.66 k allocations: 248.148 KiB, 96.65% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.1s 0.901920 seconds (990.54 k allocations: 75.653 MiB, 4.41% gc time, 82.22% compilation time) 0.773886 seconds (894.07 k allocations: 72.561 MiB, 3.03% gc time, 83.21% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.0s Test Summary: | Pass Total Time convert_ds | 5 5 0.9s 0.116398 seconds (525.76 k allocations: 50.464 MiB, 14.78% gc time, 27.83% compilation time) 0.648832 seconds (660.93 k allocations: 58.106 MiB, 2.17% gc time, 87.65% 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 0.528058 seconds (520.49 k allocations: 51.920 MiB, 86.42% gc time, 1.90% compilation time: <1% of which was recompilation) 0.524624 seconds (596.34 k allocations: 56.206 MiB, 88.06% 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 0.164400 seconds (1.56 M allocations: 81.839 MiB, 30.85% gc time, 5.20% compilation time) 0.625308 seconds (1.71 M allocations: 90.745 MiB, 5.40% gc time, 72.72% 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 6.7s Test Summary: | Pass Total Time record info | 14 14 4.8s Test Summary: | Pass Total Time write VCF | 3 3 4.3s 2.144331 seconds (5.29 M allocations: 379.580 MiB, 3.53% gc time, 56.93% compilation time) 0.978574 seconds (2.86 M allocations: 195.204 MiB, 4.45% gc time, 23.05% compilation time) 0.920752 seconds (4.89 M allocations: 358.125 MiB, 6.49% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.6s 0.978901 seconds (629.45 k allocations: 54.737 MiB, 1.67% gc time, 50.63% 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: 1%|▎ | ETA: 0:13:23 Progress: 1%|▌ | ETA: 0:13:32 Progress: 2%|▊ | ETA: 0:13:19 Progress: 2%|█ | ETA: 0:13:11 Progress: 3%|█▎ | ETA: 0:13:07 Progress: 4%|█▌ | ETA: 0:13:04 Progress: 4%|█▊ | ETA: 0:13:37 Progress: 5%|██ | ETA: 0:14:10 Progress: 5%|██▏ | ETA: 0:14:32 Progress: 6%|██▎ | ETA: 0:14:51 Progress: 6%|██▌ | ETA: 0:15:05 Progress: 6%|██▋ | ETA: 0:15:17 Progress: 7%|██▊ | ETA: 0:15:29 Progress: 7%|███ | ETA: 0:15:41 Progress: 8%|███▏ | ETA: 0:15:49 Progress: 8%|███▎ | ETA: 0:15:55 Progress: 8%|███▌ | ETA: 0:15:59 Progress: 9%|███▋ | ETA: 0:16:04 Progress: 9%|███▊ | ETA: 0:16:07 Progress: 10%|████ | ETA: 0:16:02 Progress: 10%|████▎ | ETA: 0:15:53 Progress: 11%|████▍ | ETA: 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A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 426 running 1 of 1 signal (10): User defined signal 1 jl_to_typeof at /source/src/julia.h:964 [inlined] jl_object_id__cold at /source/src/builtins.c:463 immut_id_ at /source/src/builtins.c:436 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: 0x72ddabfb8b76) at (unknown file) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 _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: 0x72dd8d5485c6) at (unknown file) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 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:1855 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_invoke at /source/src/gf.c:3805 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:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 _include at ./loading.jl:2907 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_66866.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [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:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 _include at ./loading.jl:2907 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_66866.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [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:290 _start at ./client.jl:557 jfptr__start_48366.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x72ddad2eb249) 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: 91%|█████████████████████████████████████▍ | ETA: 0:01:44┌ 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 0x000072dd93200010 Total snapshots: 703. Utilization: 100% ╎700 @Base/client.jl:557 _start() ╎ 700 @Base/client.jl:290 exec_options(opts::Base.JLOptions) ╎ 700 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 700 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 700 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 700 @Base/loading.jl:2907 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 700 @Base/loading.jl:2847 include_string(mapexpr::typeof(identity), m… ╎ ╎ 700 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 700 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 700 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 700 @Base/loading.jl:2907 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 700 @Base/loading.jl:2847 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 700 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 700 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 700 @Test/src/Test.jl:1855 macro expansion ╎ ╎ ╎ 700 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 700 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 2╎ ╎ ╎ ╎ 117 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 1 @Base/array.jl:988 setindex! 1╎ ╎ ╎ ╎ 1 @Base/array.jl:993 _setindex! 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:0 aim_select(record::VariantCallForm… ╎ ╎ ╎ ╎ 18 @VCFTools/…ct.jl:65 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 18 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 13 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 5 @Base/…ators.jl:425 > 5╎ ╎ ╎ ╎ ╎ 5 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 4 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:387 checkbounds ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:383 checkbounds 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:11 length 2╎ ╎ ╎ ╎ ╎ 2 @Base/…otion.jl:637 == 2╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:3151 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:960 _getindex 1╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:134 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:146 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @VCFTools/…s.jl:169 hwe(n00::Int64, n01::Int64, n1… ╎ ╎ ╎ ╎ ╎ 1 @Distributions/…:102 ccdf ╎ ╎ ╎ ╎ ╎ 1 @Distributions/…:649 ccdf ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/….jl:9 chisqccdf ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/…jl:50 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 1 @StatsFuns/…jl:48 gammaccdf ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:855 gamma_inc ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:855 gamma_inc ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:931 _gamma_inc(a::Floa… ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:13 erfc 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @SpecialFunctions/…:15 _erfc ╎ ╎ ╎ ╎ 85 @VCFTools/…ct.jl:74 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 83 @Base/array.jl:2458 findfirst ╎ ╎ ╎ ╎ 81 @Base/array.jl:2407 findnext ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 8╎ ╎ ╎ ╎ ╎ 8 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 72 @Base/…ators.jl:1195 Fix ╎ ╎ ╎ ╎ ╎ 72 @Base/…tors.jl:1195 #_#59 ╎ ╎ ╎ ╎ ╎ 72 @Base/…tors.jl:178 isequal 72╎ ╎ ╎ ╎ ╎ 72 @Base/…ring.jl:186 == ╎ ╎ ╎ ╎ 2 @Base/array.jl:2408 findnext 2╎ ╎ ╎ ╎ ╎ 2 @Base/…otion.jl:637 == 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 6 @VCFTools/…ct.jl:76 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 6 @VariantCallFormat/…:613 findgenokey 1╎ ╎ ╎ ╎ 1 @Base/…piler.jl:57 getproperty ╎ ╎ ╎ ╎ 5 @Base/array.jl:2458 findfirst ╎ ╎ ╎ ╎ ╎ 5 @Base/array.jl:2407 findnext ╎ ╎ ╎ ╎ ╎ 5 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 5 @VariantCallFormat/…:673 isequaldata ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:1272 pointer ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1269 pointer 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nter.jl:63 cconvert 4╎ ╎ ╎ ╎ ╎ 4 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 2 @VCFTools/…ct.jl:79 aim_select(record::VariantCallFor… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex 1╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:225 geno_ismissing ╎ ╎ ╎ ╎ 1 @VCFTools/…ct.jl:86 aim_select(record::VariantCallFor… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ct.jl:99 aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:261 log(x::Float64) ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:289 _log ╎ ╎ ╎ ╎ ╎ 1 @Base/…l/log.jl:163 log_proc1 1╎ ╎ ╎ ╎ ╎ 1 @Base/float.jl:492 + ╎ ╎ ╎ ╎ 583 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 583 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 83 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 83 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 83 @VariantCallFormat/…:147 read!(reader::VariantCall… 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1158 _growend_internal!(a::Vector{… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:160 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2083 empty! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1246 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:219 _unsetindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ 76 @VariantCallFormat/…:169 _read!(reader::VariantCa… 2╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:0 macro expansion ╎ ╎ ╎ ╎ ╎ 64 @Automa/…en.jl:263 macro expansion ╎ ╎ ╎ ╎ ╎ 22 @Base/array.jl:411 getindex 22╎ ╎ ╎ ╎ ╎ 22 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 40 @Base/array.jl:1303 push! ╎ ╎ ╎ ╎ ╎ 40 @Base/…ray.jl:1306 _push! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1170 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1171 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1173 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 36 @Base/…ray.jl:1174 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1126 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ay.jl:1149 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ay.jl:1069 array_new_memory 29╎ ╎ ╎ ╎ ╎ ╎ 29 @Base/…ot.jl:588 GenericMemory 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1157 _growend_internal!(a::Vect… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:1158 _growend_internal!(a::Vect… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:967 getindex 2╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:270 macro expansion ╎ ╎ ╎ ╎ ╎ 5 @Automa/…en.jl:291 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:56 getindex ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ry.jl:49 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:522 <= ╎ ╎ ╎ ╎ ╎ 4 @Automa/…ry.jl:57 getindex 4╎ ╎ ╎ ╎ ╎ 4 @Base/…nter.jl:151 unsafe_load 1╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:292 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Base/range.jl:1458 in 2╎ ╎ ╎ ╎ ╎ 2 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 4 @VariantCallFormat/…:185 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 4 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 4 @BufferedStreams/…:71 fillbuffer! ╎ ╎ ╎ ╎ ╎ 4 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:387 readbytes!(stream::… ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:201 eof(stream::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:582 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:596 fillbuffer(strea… ╎ ╎ ╎ ╎ ╎ ╎ 4 @TranscodingStreams/…:656 callprocess(str… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @CodecZlib/…:195 process(codec::GzipDeco… 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ 500 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 500 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 4 @Base/array.jl:360 copy 3╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:361 copy ╎ ╎ ╎ ╎ ╎ 1 @Base/…emory.jl:125 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ 1 @Base/cmem.jl:28 memmove ╎ ╎ ╎ ╎ ╎ 495 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 495 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 495 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 6╎ ╎ ╎ ╎ ╎ 495 @Base/…copy.jl:104 deepcopy_internal ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:594 memoryref 62╎ ╎ ╎ ╎ ╎ 62 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 22╎ ╎ ╎ ╎ ╎ 22 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 10╎ ╎ ╎ ╎ ╎ 10 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 30╎ ╎ ╎ ╎ ╎ 331 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:182 in 30╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 57 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/boot.jl:661 Array 9╎ ╎ ╎ ╎ ╎ ╎ 10 @Base/…ot.jl:649 Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:594 memoryref 46╎ ╎ ╎ ╎ ╎ ╎ 47 @Base/…ict.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:61 setproperty! 5╎ ╎ ╎ ╎ ╎ ╎ 210 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:57 getproperty 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 59 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 59 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 59 @Base/…ct.jl:182 in 57╎ ╎ ╎ ╎ ╎ ╎ 59 @Base/…ct.jl:92 get 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 139 @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 10╎ ╎ ╎ ╎ ╎ ╎ 109 @Base/…py.jl:104 deepcopy_internal 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:0 _deepcopy_memory_t(x::Memor… 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 16╎ ╎ ╎ ╎ ╎ ╎ 92 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ry.jl:175 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:179 copy(a::Memory{UnitRange… 14╎ ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 16 @Base/…ry.jl:180 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 16 @Base/…ry.jl:143 unsafe_copyto! 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:125 unsafe_copyto! 12╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ct.jl:81 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…rs.jl:472 >= 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:522 <= 40╎ ╎ ╎ ╎ ╎ ╎ 41 @Base/…ct.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:144 deepcopy_internal(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…on.jl:637 == 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:145 deepcopy_internal(x::Memor… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memory… 33╎ ╎ ╎ ╎ ╎ 33 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 29╎ ╎ ╎ ╎ ╎ 29 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ====================================================================================== 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:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_59164.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 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 0x00007ed4068d51e0 Total snapshots: 579. Utilization: 0% ╎579 @Base/task.jl:1150 wait_forever() 578╎ 579 @Base/task.jl:1213 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 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:1213 wait_forever at ./task.jl:1150 jfptr_wait_forever_59164.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 20645788 (Pool: 20645238; Big: 550); GC: 20 [426] 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: 0x72ddabfb8b76) at (unknown file) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 _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: 0x72dd8d5485c6) at (unknown file) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 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:1855 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_invoke at /source/src/gf.c:3805 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:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 _include at ./loading.jl:2907 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_66866.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [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:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 _include at ./loading.jl:2907 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_66866.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [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:290 _start at ./client.jl:557 jfptr__start_48366.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3798 [inlined] ijl_apply_generic at /source/src/gf.c:3998 jl_apply at /source/src/julia.h:2345 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x72ddad2eb249) 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: 19743224149 (Pool: 19743208665; Big: 15484); GC: 34875 PkgEval terminated after 2728.74s: test duration exceeded the time limit