Package evaluation to test VCFTools on Julia 1.14.0-DEV.1871 (50d44f5be7*) started at 2026-03-08T18:17:59.417 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.67s ################################################################################ # 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 v1.16.0 [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 v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.13 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [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 v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 5.6s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... [ Info: Compiling VCF parser... 16234.0 ms ✓ VariantCallFormat 5390.0 ms ✓ HypothesisTests 5548.8 ms ✓ VCFTools 3 dependencies successfully precompiled in 30 seconds. 113 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 53.09s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_DPGdRp/Project.toml` [336ed68f] CSV v0.10.16 [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 v2.7.1 [2913bbd2] StatsBase v0.34.10 [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_DPGdRp/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 v0.10.16 [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 v1.16.0 [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 v1.5.2 [08abe8d2] PrettyTables v3.2.3 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.13 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.4 [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 v8.18.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.5+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [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 3.1s Test Summary: | Pass Total Time openvcf | 4 4 2.6s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.6s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:37:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 15.381042 seconds (9.03 M allocations: 546.959 MiB, 4.41% gc time, 93.21% compilation time: 16% of which was recompilation) 0.387369 seconds (2.37 M allocations: 141.239 MiB, 6.95% gc time, 16.04% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:34:14 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.506521 seconds (3.92 M allocations: 238.279 MiB, 1.66% gc time, 87.81% compilation time) 0.437149 seconds (2.37 M allocations: 141.365 MiB, 4.92% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.3s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 2.0s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s 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 1.6s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:31:16 Progress: 0%|▏ | ETA: 0:22:47 Progress: 0%|▏ | ETA: 0:20:41 Progress: 0%|▏ | ETA: 0:19:37 Progress: 0%|▎ | ETA: 0:20:37 Progress: 1%|▎ | ETA: 0:20:03 Progress: 1%|▎ | ETA: 0:19:26 Progress: 1%|▍ | ETA: 0:19:00 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10%|████▎ | ETA: 0:16:44 Progress: 10%|████▎ | ETA: 0:16:42 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:32:21 Progress: 22%|████████▉ | ETA: 0:06:36 Progress: 43%|█████████████████▊ | ETA: 0:02:27 Progress: 65%|██████████████████████████▉ | ETA: 0:00:59 Progress: 91%|█████████████████████████████████████▏ | ETA: 0:00:12 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: 823 records are matched 240.907906 seconds (2.01 G allocations: 106.068 GiB, 13.28% gc time, 0.56% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:15:36 Progress: 0%|▏ | ETA: 0:19:21 Progress: 0%|▏ | ETA: 0:18:11 Progress: 0%|▏ | ETA: 0:17:21 Progress: 1%|▎ | ETA: 0:16:59 Progress: 1%|▎ | ETA: 0:17:38 Progress: 1%|▎ | ETA: 0:17:22 Progress: 1%|▍ | ETA: 0:17:11 Progress: 1%|▍ | ETA: 0:16:52 Progress: 1%|▌ | ETA: 0:16:34 Progress: 1%|▌ | ETA: 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ETA: 0:03:50 Progress: 53%|█████████████████████▋ | ETA: 0:01:51 Progress: 69%|████████████████████████████▏ | ETA: 0:00:57 Progress: 87%|███████████████████████████████████▋ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:02:06 [ Info: 488 records are matched 245.054667 seconds (2.01 G allocations: 106.050 GiB, 14.23% gc time, 0.32% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:37 Progress: 0%|▏ | ETA: 0:23:06 Progress: 0%|▏ | ETA: 0:21:18 Progress: 0%|▏ | ETA: 0:20:18 Progress: 0%|▎ | ETA: 0:19:40 Progress: 1%|▎ | ETA: 0:19:08 Progress: 1%|▎ | ETA: 0:20:17 Progress: 1%|▎ | ETA: 0:20:07 Progress: 1%|▍ | ETA: 0:19:43 Progress: 1%|▍ | ETA: 0:19:30 Progress: 1%|▍ | ETA: 0:19:17 Progress: 1%|▌ | ETA: 0:19:02 Progress: 1%|▌ | ETA: 0:19:40 Progress: 1%|▌ | ETA: 0:19:26 Progress: 1%|▋ | ETA: 0:19:14 Progress: 2%|▋ | ETA: 0:19:02 Progress: 2%|▋ | ETA: 0:18:50 Progress: 2%|▊ | ETA: 0:19:10 Progress: 2%|▊ | ETA: 0:19:12 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100%|█████████████████████████████████████████| Time: 0:02:06 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 23:04:04 Progress: 15%|██████▏ | ETA: 0:11:50 Progress: 31%|████████████▌ | ETA: 0:04:45 Progress: 49%|████████████████████ | ETA: 0:02:12 Progress: 67%|███████████████████████████▍ | ETA: 0:01:03 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:02:09 [ Info: 0 records are matched 266.550509 seconds (2.01 G allocations: 106.050 GiB, 15.00% gc time, 0.44% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m39.3s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:35:35 Progress: 19%|███████▊ | ETA: 0:08:43 Progress: 37%|███████████████▎ | ETA: 0:03:25 Progress: 56%|██████████████████████▉ | ETA: 0:01:38 Progress: 70%|████████████████████████████▉ | ETA: 0:00:53 Progress: 93%|██████████████████████████████████████ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:02:06 [ Info: 833 records are matched 136.364252 seconds (1.01 G allocations: 53.815 GiB, 13.31% gc time, 0.54% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:22:33 Progress: 19%|███████▋ | ETA: 0:08:48 Progress: 38%|███████████████▌ | ETA: 0:03:18 Progress: 57%|███████████████████████▎ | ETA: 0:01:34 Progress: 72%|█████████████████████████████▌ | ETA: 0:00:48 Progress: 94%|██████████████████████████████████████▌ | ETA: 0:00:08 Progress: 100%|█████████████████████████████████████████| Time: 0:02:04 [ Info: 493 records are matched 135.148197 seconds (1.01 G allocations: 53.814 GiB, 12.87% gc time, 0.53% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:35:26 Progress: 14%|█████▋ | ETA: 0:12:55 Progress: 30%|████████████▍ | ETA: 0:04:42 Progress: 50%|████████████████████▍ | ETA: 0:02:06 Progress: 69%|████████████████████████████▍ | ETA: 0:00:56 Progress: 88%|████████████████████████████████████▎ | ETA: 0:00:16 Progress: 100%|█████████████████████████████████████████| Time: 0:02:07 [ Info: 0 records are matched 136.834492 seconds (1.01 G allocations: 53.814 GiB, 13.63% gc time, 0.55% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m51.2s 1.513906 seconds (1.15 M allocations: 65.792 MiB, 86.91% compilation time) 1.277818 seconds (1.06 M allocations: 62.769 MiB, 3.58% gc time, 80.18% compilation time) 1.205690 seconds (1.06 M allocations: 61.841 MiB, 83.62% compilation time) 0.553745 seconds (175.62 k allocations: 10.178 MiB, 99.96% compilation time) 0.010750 seconds (6.10 k allocations: 393.102 KiB, 96.19% compilation time) 0.008774 seconds (2.62 k allocations: 165.695 KiB, 96.20% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 11.8s 1.286202 seconds (957.99 k allocations: 56.406 MiB, 3.67% gc time, 80.68% compilation time) 1.014447 seconds (817.18 k allocations: 50.538 MiB, 81.05% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 7.8s Test Summary: | Pass Total Time convert_ds | 5 5 1.4s 0.124246 seconds (525.04 k allocations: 30.675 MiB, 26.97% compilation time) 0.797474 seconds (625.59 k allocations: 36.988 MiB, 3.64% gc time, 85.98% 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 0.066429 seconds (520.58 k allocations: 32.160 MiB) 0.704989 seconds (583.65 k allocations: 36.186 MiB, 3.02% gc time, 86.85% 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 0.112496 seconds (1.56 M allocations: 62.080 MiB, 7.93% compilation time) 1.314085 seconds (1.68 M allocations: 69.847 MiB, 45.46% gc time, 46.20% 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 8.0s Test Summary: | Pass Total Time record info | 14 14 6.3s Test Summary: | Pass Total Time write VCF | 3 3 5.5s 2.589151 seconds (4.74 M allocations: 295.440 MiB, 4.00% gc time, 59.20% compilation time) 1.101808 seconds (2.38 M allocations: 142.375 MiB, 4.62% gc time, 24.20% compilation time) 0.955941 seconds (4.42 M allocations: 276.417 MiB, 6.41% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 8.2s 1.143960 seconds (591.58 k allocations: 33.125 MiB, 2.10% gc time, 51.30% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.4s Test Summary: | Pass Total Time filter_chr | 4 4 1.6s Progress: 0%|▏ | ETA: 0:23:25 Progress: 1%|▎ | ETA: 0:24:40 Progress: 1%|▌ | ETA: 0:23:48 Progress: 1%|▋ | ETA: 0:23:13 Progress: 2%|▊ | ETA: 0:23:29 Progress: 2%|▉ | ETA: 0:23:05 Progress: 3%|█ | ETA: 0:22:49 Progress: 3%|█▎ | ETA: 0:23:01 Progress: 3%|█▍ | ETA: 0:22:51 Progress: 4%|█▌ | ETA: 0:22:40 Progress: 4%|█▋ | ETA: 0:22:49 Progress: 4%|█▉ | ETA: 0:22:32 Progress: 5%|██ | ETA: 0:22:19 Progress: 5%|██▏ | ETA: 0:22:21 Progress: 6%|██▎ | ETA: 0:22:09 Progress: 6%|██▌ | ETA: 0:21:59 Progress: 6%|██▋ | ETA: 0:22:03 Progress: 7%|██▊ | ETA: 0:21:52 Progress: 7%|██▉ | ETA: 0:21:51 Progress: 8%|███▏ | ETA: 0:21:41 Progress: 8%|███▎ | ETA: 0:21:29 Progress: 8%|███▍ | ETA: 0:21:25 Progress: 9%|███▋ | ETA: 0:21:10 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Progress: 92%|█████████████████████████████████████▊ | ETA: 0:01:50 Progress: 92%|█████████████████████████████████████▉ | ETA: 0:01:45 ====================================================================================== 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 22 running 1 of 1 signal (10): User defined signal 1 gc_sweep_pool at /source/src/gc-stock.c:1445 [inlined] _jl_gc_collect at /source/src/gc-stock.c:3215 ijl_gc_collect at /source/src/gc-stock.c:3523 maybe_collect at /source/src/gc-stock.c:357 [inlined] jl_gc_small_alloc_inner at /source/src/gc-stock.c:734 jl_gc_small_alloc_noinline at /source/src/gc-stock.c:792 [inlined] jl_gc_alloc_ at /source/src/gc-stock.c:806 jl_alloc_genericmemory_unchecked at /source/src/genericmemory.c:41 _new_genericmemory_ at /source/src/genericmemory.c:69 [inlined] jl_alloc_genericmemory at /source/src/genericmemory.c:102 ijl_idtable_rehash at /source/src/iddict.c:22 jl_table_assign_bp at /source/src/iddict.c:101 [inlined] ijl_eqtable_put at /source/src/iddict.c:146 setindex! at ./iddict.jl:86 [inlined] _deepcopy_memory_t at ./deepcopy.jl:109 _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_invoke at /source/src/gf.c:4120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x7b7d87bb4496) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 _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: 0x7b7d79dccba6) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 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:2243 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 jl_invoke_oneshot at /source/src/gf.c:4148 ijl_eval_thunk at /source/src/toplevel.c:758 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 include_string at ./loading.jl:3131 _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 _include at ./loading.jl:3191 include at ./Base.jl:324 IncludeInto at ./Base.jl:325 unknown function (ip: 0x7b7d87afe0e2) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:766 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 include_string at ./loading.jl:3131 _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 _include at ./loading.jl:3191 include at ./Base.jl:324 IncludeInto at ./Base.jl:325 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:766 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [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: 0x7b7da208a249) 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: 93%|██████████████████████████████████████ | ETA: 0:01:40┌ 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 0x00007b7d87bfc010 Total snapshots: 470. Utilization: 100% ╎469 @Base/client.jl:585 _start() ╎ 469 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 469 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ 469 @Base/Base.jl:325 (::Base.IncludeInto)(fname::String) ╎ 469 @Base/Base.jl:324 include(mapexpr::Function, mod::Module, _path::St… ╎ 469 @Base/loading.jl:3191 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 469 @Base/loading.jl:3131 include_string(mapexpr::typeof(identity), m… ╎ ╎ 469 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ 469 @Base/Base.jl:325 (::Base.IncludeInto)(fname::String) ╎ ╎ 469 @Base/Base.jl:324 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 469 @Base/loading.jl:3191 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 469 @Base/loading.jl:3131 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 469 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ ╎ 469 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 469 @Test/src/Test.jl:2243 macro expansion ╎ ╎ ╎ 469 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 469 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 2╎ ╎ ╎ ╎ 67 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 14 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 14 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:123 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2449 findnext ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:1026 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:385 checkbounds ╎ ╎ ╎ ╎ 12 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 6╎ ╎ ╎ ╎ ╎ 6 @Base/…tials.jl:1027 getindex ╎ ╎ ╎ ╎ ╎ 3 @Base/…ators.jl:424 > 3╎ ╎ ╎ ╎ ╎ 3 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 3 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:1026 getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:385 checkbounds ╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:381 checkbounds 2╎ ╎ ╎ ╎ ╎ 2 @Base/…als.jl:1242 length 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tion.jl:637 == ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:135 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 44 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 41 @Base/array.jl:2500 findfirst ╎ ╎ ╎ ╎ 41 @Base/array.jl:2449 findnext 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:1027 getindex ╎ ╎ ╎ ╎ ╎ 38 @Base/…ators.jl:1203 Fix ╎ ╎ ╎ ╎ ╎ 38 @Base/…tors.jl:1203 #_#57 ╎ ╎ ╎ ╎ ╎ 38 @Base/…tors.jl:178 isequal 38╎ ╎ ╎ ╎ ╎ 38 @Base/…ring.jl:187 == 3╎ ╎ ╎ ╎ 3 @Base/…ntials.jl:1027 getindex ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 3 @Base/array.jl:2500 findfirst 1╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:2449 findnext ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:673 isequaldata 2╎ ╎ ╎ ╎ ╎ 2 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:78 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1026 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1026 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:1027 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:45 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:483 next! ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:484 #next!#15 ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:465 lock_if_threading 1╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:453 is_threading ╎ ╎ ╎ ╎ 401 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 401 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 49 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 49 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 49 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 32 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 30 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 12 @Base/array.jl:436 getindex 12╎ ╎ ╎ ╎ ╎ 12 @Base/boot.jl:715 Array ╎ ╎ ╎ ╎ ╎ 17 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 15 @Base/…ray.jl:1348 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1201 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:1213 + 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1202 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1204 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 1╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ray.jl:1205 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1159 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:58 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ay.jl:1181 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ay.jl:1101 array_new_memory 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ot.jl:654 GenericMemory 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1190 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1349 _push! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1044 __safe_setindex! ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:215 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:49 resize_and_copy! ╎ ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:55 resize_and_copy! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1540 resize!(a::Vector{UInt8}, … ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1201 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:1213 + ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:503 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1465 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:14 & ╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:571 macro expansion 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:1213 + ╎ ╎ ╎ ╎ ╎ 17 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 17 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 17 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 17 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/io.jl:1170 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 14 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/io.jl:368 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:298 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:206 eof ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:52 buffersize 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:58 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 13 @TranscodingStreams/…:302 peek 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…er.jl:58 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:1026 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:385 checkbounds 9╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ls.jl:1027 getindex ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/io.jl:1176 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:393 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1020 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 352 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 352 @VariantCallFormat/…:309 copy(record::VariantCallFo… 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:386 copy ╎ ╎ ╎ ╎ ╎ 351 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 1 @Base/…pcopy.jl:129 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tdict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:182 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:92 get ╎ ╎ ╎ ╎ ╎ 350 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 350 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 1╎ ╎ ╎ ╎ ╎ 350 @Base/…copy.jl:104 deepcopy_internal ╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:654 GenericMemory ╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:660 memoryref 45╎ ╎ ╎ ╎ ╎ 45 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 3╎ ╎ ╎ ╎ ╎ 3 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 8╎ ╎ ╎ ╎ ╎ 8 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:883 isbits 13╎ ╎ ╎ ╎ ╎ 233 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:128 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ct.jl:182 in 28╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 36 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/boot.jl:727 Array ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:714 Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:654 GenericMemory 6╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ot.jl:715 Array 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:660 memoryref 24╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ict.jl:86 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ler.jl:62 setproperty! 1╎ ╎ ╎ ╎ ╎ ╎ 154 @Base/…opy.jl:133 deepcopy_internal(x::Vector… 3╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 42 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 42 @Base/…ict.jl:19 haskey 1╎ ╎ ╎ ╎ ╎ ╎ 42 @Base/…ct.jl:182 in 41╎ ╎ ╎ ╎ ╎ ╎ 41 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 105 @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 22╎ ╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:93 get 5╎ ╎ ╎ ╎ ╎ ╎ 82 @Base/…py.jl:104 deepcopy_internal 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… 10╎ ╎ ╎ ╎ ╎ ╎ 74 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ry.jl:193 copy(a::Memory{UnitRange… 9╎ ╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ot.jl:654 GenericMemory 1╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:194 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ry.jl:157 unsafe_copyto! 7╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ot.jl:661 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ry.jl:139 unsafe_copyto! 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…em.jl:28 memmove 35╎ ╎ ╎ ╎ ╎ ╎ 40 @Base/…ct.jl:86 setindex! 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…er.jl:62 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ct.jl:87 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…er.jl:62 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:144 deepcopy_internal(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…on.jl:637 == 47╎ ╎ ╎ ╎ ╎ 47 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 8╎ ╎ ╎ ╎ ╎ 8 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1246 wait_forever at ./task.jl:1168 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007aa5ea49ba30 Total snapshots: 400. Utilization: 0% ╎400 @Base/task.jl:1168 wait_forever() 399╎ 400 @Base/task.jl:1246 wait() Progress: 93%|██████████████████████████████████████▎ | ETA: 0:01:32 [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 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_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) Allocations: 19503387 (Pool: 19502693; Big: 694); GC: 15 [22] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 eof at /home/pkgeval/.julia/packages/TranscodingStreams/O3BYF/src/stream.jl:209 [inlined] readbytes! at ./io.jl:1169 readbytes! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/io.jl:5 [inlined] fillbuffer! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/bufferedinputstream.jl:71 fillbuffer! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/bufferedinputstream.jl:61 [inlined] _read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:181 _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 read! at /home/pkgeval/.julia/packages/VariantCallFormat/tQ143/src/ReaderHelper.jl:142 tryread! at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:76 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:87 [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: 0x7b7d79dccba6) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 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:2243 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 jl_invoke_oneshot at /source/src/gf.c:4148 ijl_eval_thunk at /source/src/toplevel.c:758 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 include_string at ./loading.jl:3131 _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 _include at ./loading.jl:3191 include at ./Base.jl:324 IncludeInto at ./Base.jl:325 unknown function (ip: 0x7b7d87afe0e2) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:766 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 include_string at ./loading.jl:3131 _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 _include at ./loading.jl:3191 include at ./Base.jl:324 IncludeInto at ./Base.jl:325 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [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:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 ijl_eval_thunk at /source/src/toplevel.c:766 jl_toplevel_eval_flex at /source/src/toplevel.c:712 jl_eval_toplevel_stmts at /source/src/toplevel.c:602 jl_toplevel_eval_flex at /source/src/toplevel.c:684 ijl_toplevel_eval at /source/src/toplevel.c:780 ijl_toplevel_eval_in at /source/src/toplevel.c:825 eval at ./boot.jl:517 exec_options at ./client.jl:310 _start at ./client.jl:585 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [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: 0x7b7da208a249) 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: 18195936357 (Pool: 18195920889; Big: 15468); GC: 17083 PkgEval terminated after 2722.33s: test duration exceeded the time limit