Package evaluation to test VCFTools on Julia 1.14.0-DEV.1354 (1806b0bc31*) started at 2025-12-14T17:07:26.236 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.39s ################################################################################ # 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 v0.2.4 [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 v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [4c63d2b9] + StatsFuns v1.5.2 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 4.51s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 13.25s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_DaUCkb/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.9 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_DaUCkb/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 7.0s Test Summary: | Pass Total Time openvcf | 4 4 3.0s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 1.8s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.2s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:21:50 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 10.989013 seconds (9.97 M allocations: 564.232 MiB, 2.03% gc time, 94.91% compilation time: 22% of which was recompilation) 0.452504 seconds (2.40 M allocations: 143.649 MiB, 14.63% gc time, 17.34% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:19:44 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.145830 seconds (4.02 M allocations: 238.912 MiB, 2.67% gc time, 81.49% compilation time) 0.416969 seconds (2.38 M allocations: 143.346 MiB, 6.38% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 17.0s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.1s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 1.9s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.7s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 4.3s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:07 Progress: 0%|▏ | ETA: 0:17:41 Progress: 0%|▏ | ETA: 0:17:28 Progress: 0%|▏ | ETA: 0:17:12 Progress: 0%|▎ | ETA: 0:17:01 Progress: 1%|▎ | ETA: 0:16:49 Progress: 1%|▎ | ETA: 0:16:47 Progress: 1%|▍ | ETA: 0:16:46 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Progress: 100%|█████████████████████████████████████████| Time: 0:01:43 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:55:15 Progress: 20%|████████▍ | ETA: 0:06:39 Progress: 41%|████████████████▉ | ETA: 0:02:27 Progress: 63%|█████████████████████████▉ | ETA: 0:01:01 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 823 records are matched 219.356425 seconds (2.01 G allocations: 106.139 GiB, 6.67% gc time, 0.45% compilation time: 8% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:57 Progress: 0%|▏ | ETA: 0:17:35 Progress: 0%|▏ | ETA: 0:17:25 Progress: 0%|▏ | ETA: 0:17:13 Progress: 0%|▎ | ETA: 0:17:08 Progress: 1%|▎ | ETA: 0:17:02 Progress: 1%|▎ | ETA: 0:17:03 Progress: 1%|▍ | ETA: 0:17:05 Progress: 1%|▍ | ETA: 0:17:05 Progress: 1%|▍ | ETA: 0:17:05 Progress: 1%|▌ | ETA: 0:17:04 Progress: 1%|▌ | ETA: 0:17:05 Progress: 1%|▌ | ETA: 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9%|███▌ | ETA: 0:18:10 Progress: 9%|███▋ | ETA: 0:18:09 Progress: 9%|███▋ | ETA: 0:18:08 Progress: 9%|███▋ | ETA: 0:18:07 Progress: 9%|███▋ | ETA: 0:18:06 Progress: 9%|███▊ | ETA: 0:18:05 Progress: 9%|███▊ | ETA: 0:18:04 Progress: 9%|███▊ | ETA: 0:18:03 Progress: 9%|███▉ | ETA: 0:18:01 Progress: 9%|███▉ | ETA: 0:18:00 Progress: 9%|███▉ | ETA: 0:17:59 Progress: 10%|███▉ | ETA: 0:17:58 Progress: 10%|████ | ETA: 0:17:57 Progress: 10%|████ | ETA: 0:17:56 Progress: 10%|████ | ETA: 0:17:55 Progress: 10%|████▏ | ETA: 0:17:54 Progress: 10%|████▏ | ETA: 0:17:53 Progress: 10%|████▏ | ETA: 0:17:52 Progress: 10%|████▏ | ETA: 0:17:51 Progress: 10%|████▎ | ETA: 0:17:49 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 23:19:08 Progress: 16%|██████▌ | ETA: 0:11:03 Progress: 35%|██████████████▏ | ETA: 0:03:58 Progress: 54%|██████████████████████▏ | ETA: 0:01:48 Progress: 73%|██████████████████████████████ | ETA: 0:00:47 Progress: 94%|██████████████████████████████████████▋ | ETA: 0:00:08 Progress: 100%|█████████████████████████████████████████| Time: 0:02:09 [ Info: 0 records are matched 262.933276 seconds (2.01 G allocations: 106.120 GiB, 7.28% gc time, 0.31% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m14.8s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:52:52 Progress: 20%|████████▏ | ETA: 0:07:33 Progress: 41%|████████████████▉ | ETA: 0:02:42 Progress: 62%|█████████████████████████▌ | ETA: 0:01:09 Progress: 85%|██████████████████████████████████▉ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 833 records are matched 125.743690 seconds (1.02 G allocations: 53.885 GiB, 7.33% gc time, 0.47% compilation time: <1% of which was recompilation) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:52:05 Progress: 18%|███████▍ | ETA: 0:08:52 Progress: 37%|███████████████▍ | ETA: 0:03:18 Progress: 58%|███████████████████████▉ | ETA: 0:01:25 Progress: 79%|████████████████████████████████▌ | ETA: 0:00:31 Progress: 98%|████████████████████████████████████████▎| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 493 records are matched 131.510048 seconds (1.02 G allocations: 53.885 GiB, 7.04% gc time, 0.44% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:08:36 Progress: 28%|███████████▋ | ETA: 0:04:46 Progress: 57%|███████████████████████▎ | ETA: 0:01:28 Progress: 85%|██████████████████████████████████▉ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 0 records are matched 125.650186 seconds (1.02 G allocations: 53.884 GiB, 7.26% gc time, 0.46% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m25.2s 0.812526 seconds (1.26 M allocations: 68.105 MiB, 5.34% gc time, 87.37% compilation time) 0.698277 seconds (1.15 M allocations: 64.080 MiB, 81.89% compilation time) 0.695332 seconds (1.15 M allocations: 63.111 MiB, 4.61% gc time, 85.74% compilation time) 0.269689 seconds (206.38 k allocations: 10.765 MiB, 99.95% compilation time) 0.009996 seconds (6.46 k allocations: 394.180 KiB, 97.03% compilation time) 0.007823 seconds (2.65 k allocations: 165.414 KiB, 97.12% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 5.8s 0.553137 seconds (973.46 k allocations: 54.440 MiB, 5.59% gc time, 76.54% compilation time) 0.467802 seconds (876.85 k allocations: 51.602 MiB, 79.50% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 3.2s Test Summary: | Pass Total Time convert_ds | 5 5 0.6s 0.083924 seconds (525.74 k allocations: 30.690 MiB, 41.20% compilation time) 0.357886 seconds (643.96 k allocations: 37.249 MiB, 4.66% gc time, 83.44% compilation time) ┌ Warning: Reached end of reader; columns 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:72 ┌ Warning: Reached end of reader; rows 1357-1400 are set to missing values └ @ VCFTools ~/.julia/packages/VCFTools/IWkMe/src/convert.jl:176 0.056676 seconds (520.58 k allocations: 32.160 MiB, 29.72% gc time) 0.270093 seconds (595.44 k allocations: 36.387 MiB, 84.92% 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 0.095098 seconds (1.56 M allocations: 62.080 MiB, 18.36% gc time, 7.30% compilation time) 0.424840 seconds (1.71 M allocations: 70.265 MiB, 15.68% gc time, 67.88% 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 3.7s Test Summary: | Pass Total Time record info | 14 14 2.4s Test Summary: | Pass Total Time write VCF | 3 3 2.0s 1.497785 seconds (4.80 M allocations: 296.395 MiB, 3.60% gc time, 46.49% compilation time) 0.894754 seconds (2.39 M allocations: 142.823 MiB, 3.70% gc time, 19.26% compilation time) 0.836279 seconds (4.42 M allocations: 276.456 MiB, 6.06% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 5.3s 0.718181 seconds (604.89 k allocations: 33.383 MiB, 2.37% gc time, 36.03% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 2.2s Test Summary: | Pass Total Time filter_chr | 4 4 1.2s Progress: 0%|▏ | ETA: 0:23:08 Progress: 1%|▍ | ETA: 0:21:06 Progress: 1%|▌ | ETA: 0:20:42 Progress: 2%|▋ | ETA: 0:20:09 Progress: 2%|▉ | ETA: 0:19:40 Progress: 3%|█ | ETA: 0:19:34 Progress: 3%|█▎ | ETA: 0:19:26 Progress: 3%|█▍ | ETA: 0:19:19 Progress: 4%|█▌ | ETA: 0:19:14 Progress: 4%|█▊ | ETA: 0:19:08 Progress: 5%|█▉ | ETA: 0:19:01 Progress: 5%|██▏ | ETA: 0:18:52 Progress: 6%|██▎ | ETA: 0:18:35 Progress: 6%|██▌ | ETA: 0:18:33 Progress: 6%|██▋ | ETA: 0:18:30 Progress: 7%|██▉ | ETA: 0:18:37 Progress: 7%|███ | ETA: 0:18:44 Progress: 8%|███▏ | ETA: 0:18:49 Progress: 8%|███▎ | ETA: 0:18:53 Progress: 8%|███▍ | ETA: 0:18:55 Progress: 9%|███▌ | ETA: 0:18:55 Progress: 9%|███▊ | ETA: 0:18:57 Progress: 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99%|████████████████████████████████████████▌| ETA: 0:00:16 Progress: 99%|████████████████████████████████████████▋| ETA: 0:00:11 Progress: 99%|████████████████████████████████████████▉| ETA: 0:00:06 Progress: 99%|█████████████████████████████████████████| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:23:17 Test Summary: | Pass Total Time AIM selection | 4 4 23m37.7s ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 9 running 1 of 1 signal (10): User defined signal 1 _ZNK4llvm4Loop22isRecursivelyLCSSAFormERKNS_13DominatorTreeERKNS_8LoopInfoEb at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZNK4llvm19PassInstrumentation12runAfterPassINS_4LoopENS_6detail11PassConceptIS2_NS_15AnalysisManagerIS2_JRNS_27LoopStandardAnalysisResultsEEEEJS7_RNS_10LPMUpdaterEEEEEEvRKT0_RKT_RKNS_17PreservedAnalysesE.isra.0 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) unknown function (ip: (nil)) at (unknown file) #= 16.8 ms =# precompile(Tuple{typeof(Base.getproperty), Random.SamplerTag{Ref{NTuple{4, UInt64}}, Tuple{Random.SamplerType{UInt64}}, NTuple{4, UInt64}}, Symbol}) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Test Summary: | Pass Total Time┌ 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 0x0000722fa49fc010 Total snapshots: 445. Utilization: 100% ╎436 @Base/client.jl:577 _start() ╎ 436 @Base/client.jl:310 exec_options(opts::Base.JLOptions) ╎ 436 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 436 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 436 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 436 @Base/loading.jl:3152 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 436 @Base/loading.jl:3092 include_string(mapexpr::typeof(identity), m… ╎ ╎ 436 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 436 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 436 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 436 @Base/loading.jl:3152 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 436 @Base/loading.jl:3092 include_string(mapexpr::typeof(identit… 42╎ ╎ ╎ 436 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 31 @Compiler/…nfer.jl:1719 typeinf_ext_toplevel(mi::Core.Meth… ╎ ╎ ╎ 27 @Compiler/…nfer.jl:1710 typeinf_ext_toplevel ╎ ╎ ╎ 27 @Compiler/…fer.jl:1527 typeinf_ext(interp::Compiler.Nati… ╎ ╎ ╎ ╎ 5 @Compiler/…ion.jl:4492 typeinf(interp::Compiler.NativeI… ╎ ╎ ╎ ╎ 5 @Compiler/…te.jl:1206 doworkloop(interp::Compiler.Nati… ╎ ╎ ╎ ╎ 5 @Compiler/…on.jl:177 (::Compiler.var"#handle1#abstrac… ╎ ╎ ╎ ╎ 5 @Compiler/…on.jl:858 abstract_call_method_with_const… ╎ ╎ ╎ ╎ 4 @Compiler/…on.jl:864 abstract_call_method_with_cons… 3╎ ╎ ╎ ╎ ╎ 4 @Compiler/…n.jl:999 concrete_eval_call(interp::Com… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:1719 typeinf_ext_toplevel(mi::Core… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:1711 typeinf_ext_toplevel 1╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:1704 add_codeinsts_to_jit!(inter… ╎ ╎ ╎ ╎ 1 @Compiler/…on.jl:889 abstract_call_method_with_cons… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…n.jl:1340 const_prop_call(interp::Compi… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:4508 typeinf(interp::Compiler.Nati… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:278 finish_nocycle(interp::Compil… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:1021 optimize(interp::Compiler.N… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…jl:1048 run_passes_ipo_safe ╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…jl:1035 run_passes_ipo_safe(ci::Co… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…jl:79 ssa_inlining_pass! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…l:260 finish_cfg_inline!(state::… ╎ ╎ ╎ ╎ 16 @Compiler/…ion.jl:4501 typeinf(interp::Compiler.NativeI… ╎ ╎ ╎ ╎ 14 @Compiler/…on.jl:4344 typeinf_local(interp::Compiler.N… ╎ ╎ ╎ ╎ 14 @Compiler/…on.jl:3795 abstract_eval_basic_statement ╎ ╎ ╎ ╎ 14 @Compiler/…on.jl:3838 abstract_eval_basic_statement ╎ ╎ ╎ ╎ 14 @Compiler/…n.jl:3439 abstract_eval_statement_expr(i… ╎ ╎ ╎ ╎ ╎ 14 @Compiler/…n.jl:3075 abstract_eval_call ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:3052 abstract_call(interp::Compile… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…n.jl:12 call_result_unused 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 13 @Compiler/….jl:3057 abstract_call(interp::Compile… ╎ ╎ ╎ ╎ ╎ 13 @Compiler/….jl:2897 abstract_call ╎ ╎ ╎ ╎ ╎ 13 @Compiler/….jl:2904 abstract_call(interp::Compi… ╎ ╎ ╎ ╎ ╎ 13 @Compiler/…jl:2796 abstract_call_known(interp:… ╎ ╎ ╎ ╎ ╎ ╎ 8 @Compiler/…jl:119 abstract_call_gf_by_type(in… ╎ ╎ ╎ ╎ ╎ ╎ 8 @Compiler/…jl:332 find_method_matches ╎ ╎ ╎ ╎ ╎ ╎ 8 @Compiler/…l:338 #find_method_matches#131 ╎ ╎ ╎ ╎ ╎ ╎ 7 @Compiler/…l:376 find_simple_method_matche… ╎ ╎ ╎ ╎ ╎ ╎ 7 @Compiler/…l:102 findall ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Compiler/…l:105 findall(sig::Type, tabl… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Compiler/…l:70 findall ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Compiler/…l:70 #findall#5 ╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Compiler/…l:97 _findall 7╎ ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ls.jl:1603 _methods_by_ftype ╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…l:384 find_simple_method_matche… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…l:62 Compiler.MethodMatchInfo(… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:676 Array ╎ ╎ ╎ ╎ ╎ ╎ 5 @Compiler/…jl:328 abstract_call_gf_by_type(in… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Compiler/…jl:166 (::Compiler.var"#infercall… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Compiler/…l:725 abstract_call_method(inter… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Compiler/…l:1109 typeinf_edge(interp::Com… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ls.jl:1777 specialize_method 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ls.jl:1790 #specialize_method#8 ╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…jl:321 (::Compiler.var"#infercall… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…l:308 (::Compiler.var"#infercall… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…l:161 get_compileable_sig ╎ ╎ ╎ ╎ 1 @Compiler/…on.jl:4354 typeinf_local(interp::Compiler.N… ╎ ╎ ╎ ╎ 1 @Compiler/…on.jl:4119 update_exc_bestguess!(interp::C… ╎ ╎ ╎ ╎ 1 @Compiler/…ts.jl:496 tmerge(lattice::Compiler.Infere… ╎ ╎ ╎ ╎ 1 @Compiler/…ts.jl:576 tmerge ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…s.jl:721 tmerge(lattice::Compiler.Parti… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…s.jl:733 tmerge ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:749 tmerge(lattice::Compiler.JLTy… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:802 tmerge_types_slow(typea::Typ… ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:398 falses ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:400 falses ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:377 fill!(B::BitVector, x::Boo… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:359 fill! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:0 _fill! ╎ ╎ ╎ ╎ 1 @Compiler/…on.jl:4384 typeinf_local(interp::Compiler.N… ╎ ╎ ╎ ╎ 1 @Compiler/…te.jl:786 record_ssa_assign!(𝕃ᵢ::Compiler.… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 6 @Compiler/…ion.jl:4508 typeinf(interp::Compiler.NativeI… ╎ ╎ ╎ ╎ 1 @Compiler/…fer.jl:275 finish_nocycle(interp::Compiler.… ╎ ╎ ╎ ╎ 1 @Compiler/…er.jl:684 finishinfer!(me::Compiler.Infere… ╎ ╎ ╎ ╎ 1 @Compiler/…er.jl:899 type_annotate!(::Compiler.Nativ… ╎ ╎ ╎ ╎ 1 @Compiler/…er.jl:850 record_slot_assign!(sv::Compil… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 4 @Compiler/…fer.jl:278 finish_nocycle(interp::Compiler.… ╎ ╎ ╎ ╎ 4 @Compiler/…ze.jl:1021 optimize(interp::Compiler.Nativ… ╎ ╎ ╎ ╎ 4 @Compiler/…ze.jl:1048 run_passes_ipo_safe ╎ ╎ ╎ ╎ 3 @Compiler/…e.jl:1035 run_passes_ipo_safe(ci::Core.C… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…e.jl:1329 slot2reg ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…r.jl:476 construct_domtree ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:477 construct_domtree ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:242 construct_domtree(blocks::Ve… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:238 GenericDomTree ╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:90 Compiler.DFSTree(n_blocks::… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:698 Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:676 Array ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…s.jl:2110 adce_pass!(ir::Compiler.IRCod… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…r.jl:807 IncrementalCompact ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:736 CFGTransformState!(blocks::Ve… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:242 construct_domtree(blocks::Ve… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:260 update_domtree! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…jl:266 compute_domtree_nodes!(domt… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…s.jl:1552 sroa_pass!(ir::Compiler.IRCod… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:2107 non_dce_finish!(compact::Comp… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:2057 just_fixup! ╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:2081 just_fixup!(compact::Compil… 1╎ ╎ ╎ ╎ ╎ 1 @Compiler/….jl:0 fixup_node(compact::Compiler.… ╎ ╎ ╎ ╎ 1 @Compiler/…e.jl:1070 run_passes_ipo_safe(ci::Core.C… ╎ ╎ ╎ ╎ ╎ 1 @Compiler/…y.jl:433 verify_ir(ir::Compiler.IRCode,… 1╎ ╎ ╎ ╎ ╎ 1 @Compiler/…y.jl:30 check_op(ir::Compiler.IRCode, … ╎ ╎ ╎ ╎ 1 @Compiler/…fer.jl:285 finish_nocycle(interp::Compiler.… ╎ ╎ ╎ ╎ 1 @Compiler/…er.jl:145 finish!(interp::Compiler.NativeI… ╎ ╎ ╎ ╎ 1 @Compiler/…er.jl:482 transform_result_for_cache(inte… 1╎ ╎ ╎ ╎ 1 @Compiler/…ze.jl:296 ir_to_codeinf! ╎ ╎ ╎ 4 @Compiler/…nfer.jl:1711 typeinf_ext_toplevel 4╎ ╎ ╎ 4 @Compiler/…fer.jl:1704 add_codeinsts_to_jit!(interp::Com… ╎ ╎ ╎ 362 @VCFTools/…/grm.jl:19 kwcall(::@NamedTuple{method::Symbol}… ╎ ╎ ╎ 177 @VCFTools/…/grm.jl:29 grm(vcffile::String; method::Symbol… ╎ ╎ ╎ 177 @VCFTools/…vert.jl:262 convert_gt ╎ ╎ ╎ ╎ 160 @VCFTools/…ert.jl:0 convert_gt(t::Type{Float64}, vcffil… ╎ ╎ ╎ ╎ 160 @VCFTools/…ert.jl:52 kwcall(::@NamedTuple{model::Symbo… ╎ ╎ ╎ ╎ 4 @VCFTools/…rt.jl:67 copy_gt!(A::Matrix{Union{Missing,… ╎ ╎ ╎ ╎ 4 @Base/…ecated.jl:214 ProgressMeter.Progress(n::Int64… ╎ ╎ ╎ ╎ 4 @Base/…ecated.jl:214 ProgressMeter.Progress(n::Int6… ╎ ╎ ╎ ╎ ╎ 4 @Base/…cated.jl:215 ProgressMeter.Progress(n::Int6… ╎ ╎ ╎ ╎ ╎ 4 @Base/…cated.jl:252 depwarn ╎ ╎ ╎ ╎ ╎ 4 @Base/…ated.jl:257 #depwarn#975 ╎ ╎ ╎ ╎ ╎ 4 @Base/…tion.jl:1357 invokelatest_gr ╎ ╎ ╎ ╎ ╎ 4 @Base/…ion.jl:1363 #invokelatest_gr#224 ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ted.jl:266 _depwarn(msg::Any, funcsym:… ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ing.jl:403 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ed.jl:271 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ed.jl:291 firstcaller ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ed.jl:296 firstcaller 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…es.jl:110 lookup(pointer::Ptr{Not… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…es.jl:121 lookup(pointer::Ptr{Not… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:980 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:71 copy_gt!(A::Matrix{Union{Missing,… 1╎ ╎ ╎ ╎ 1 @BioGenerics/…jl:37 eof(io::VariantCallFormat.Reader) ╎ ╎ ╎ ╎ 146 @VCFTools/…rt.jl:77 copy_gt!(A::Matrix{Union{Missing,… ╎ ╎ ╎ ╎ 146 @VariantCallFormat/…:142 read!(reader::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:160 _read!(reader::VariantCall… ╎ ╎ ╎ ╎ 73 @VariantCallFormat/…:165 _read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 54 @Automa/…gen.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 37 @Base/array.jl:436 getindex 37╎ ╎ ╎ ╎ ╎ 37 @Base/boot.jl:676 Array ╎ ╎ ╎ ╎ ╎ 16 @Base/array.jl:1345 push! ╎ ╎ ╎ ╎ ╎ 15 @Base/array.jl:1348 _push! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1202 _growend! ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1204 _growend! 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 4╎ ╎ ╎ ╎ ╎ 13 @Base/array.jl:1205 _growend! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1180 _growend_internal!(a::Vecto… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ion.jl:648 max 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:844 ifelse ╎ ╎ ╎ ╎ ╎ 6 @Base/…ray.jl:1181 _growend_internal!(a::Vecto… ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ray.jl:1101 array_new_memory 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:615 GenericMemory 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1190 _growend_internal!(a::Vecto… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1349 _push! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1044 __safe_setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @Automa/…gen.jl:464 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:424 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…gen.jl:503 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…gen.jl:572 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…ayops.jl:51 vload ╎ ╎ ╎ ╎ ╎ 1 @SIMD/…sics.jl:477 load 1╎ ╎ ╎ ╎ ╎ 1 @SIMD/…sics.jl:486 macro expansion 2╎ ╎ ╎ ╎ ╎ 4 @Automa/…gen.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…mdvec.jl:491 all ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:486 reduce ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…sics.jl:1050 reduce_and 2╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:1065 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…gen.jl:583 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Automa/…ory.jl:57 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…nter.jl:151 unsafe_load 7╎ ╎ ╎ ╎ ╎ 11 @Automa/…gen.jl:584 macro expansion ╎ ╎ ╎ ╎ ╎ 4 @Base/range.jl:1454 in 4╎ ╎ ╎ ╎ ╎ 4 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:167 _read!(reader::VariantCall… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…mpiler.jl:61 setproperty! ╎ ╎ ╎ ╎ 71 @VariantCallFormat/…:181 _read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 71 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 71 @BufferedStreams/…:71 fillbuffer!(stream::Buffere… ╎ ╎ ╎ ╎ ╎ 71 @BufferedStreams/…:5 readbytes! 11╎ ╎ ╎ ╎ ╎ 11 @Base/io.jl:0 readbytes!(s::TranscodingStreams.… ╎ ╎ ╎ ╎ ╎ 33 @Base/io.jl:1167 readbytes!(s::TranscodingStrea… 7╎ ╎ ╎ ╎ ╎ 7 @TranscodingStreams/…:209 eof 2╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ 24 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 24 @TranscodingStreams/…:222 sloweof(stream::Tra… ╎ ╎ ╎ ╎ ╎ ╎ 24 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:623 fillbuffer(stream… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:741 readdata!(input:… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:43 eof(s::IOStream) 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…am.jl:262 _eof_nolock ╎ ╎ ╎ ╎ ╎ ╎ 23 @TranscodingStreams/…:624 fillbuffer(stream… ╎ ╎ ╎ ╎ ╎ ╎ 22 @TranscodingStreams/…:685 callprocess(stre… ╎ ╎ ╎ ╎ ╎ ╎ 22 @CodecZlib/…:195 process(codec::GzipDecom… 22╎ ╎ ╎ ╎ ╎ ╎ ╎ 22 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:686 callprocess(stre… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ng.jl:404 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ng.jl:342 current_logger_for_env ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ng.jl:538 current_logstate ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…es.jl:213 get ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ct.jl:1002 get(dict::Base.Pers… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…mt.jl:93 HashState 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:897 objectid ╎ ╎ ╎ ╎ ╎ 23 @Base/io.jl:1168 readbytes!(s::TranscodingStrea… ╎ ╎ ╎ ╎ ╎ 8 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/io.jl:366 peek ╎ ╎ ╎ ╎ ╎ ╎ 6 @TranscodingStreams/…:298 peek 3╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:209 eof 3╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:212 eof ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:302 peek 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 15 @TranscodingStreams/…:307 read ╎ ╎ ╎ ╎ ╎ ╎ 15 @TranscodingStreams/…:97 consumed! ╎ ╎ ╎ ╎ ╎ ╎ 15 @TranscodingStreams/…:98 #consumed!#1 15╎ ╎ ╎ ╎ ╎ ╎ 15 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1170 readbytes!(s::TranscodingStrea… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tors.jl:424 > 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 3 @Base/io.jl:1174 readbytes!(s::TranscodingStrea… ╎ ╎ ╎ ╎ ╎ 3 @Base/…rray.jl:393 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:1020 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:93 copy_gt!(A::Matrix{Union{Missing,… ╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:122 gtstats 1╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:3196 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:943 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:99 copy_gt!(A::Matrix{Union{Missing,… 1╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:225 geno_ismissing ╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:108 copy_gt!(A::Matrix{Union{Missing… ╎ ╎ ╎ ╎ 2 @Base/array.jl:3196 getindex 1╎ ╎ ╎ ╎ 2 @Base/range.jl:956 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:943 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:560 <= ╎ ╎ ╎ ╎ 3 @VCFTools/…rt.jl:110 copy_gt!(A::Matrix{Union{Missing… ╎ ╎ ╎ ╎ 1 @Base/array.jl:1031 setindex! 1╎ ╎ ╎ ╎ 1 @Base/array.jl:1037 _setindex! ╎ ╎ ╎ ╎ 2 @VCFTools/…rt.jl:11 convert_gt ╎ ╎ ╎ ╎ 2 @Base/number.jl:7 convert 2╎ ╎ ╎ ╎ ╎ 2 @Base/float.jl:245 Float64 ╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:118 copy_gt!(A::Matrix{Union{Missing… ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:483 next! ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:484 #next!#15 ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:470 lock_if_threading ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:486 #17 ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:211 updateProgress! ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:213 #updateProgress!#9 ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:217 _updateProgress! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:0 _updateProgress!(p::Progre… ╎ ╎ ╎ ╎ 1 @VCFTools/…ert.jl:273 convert_gt(t::Type{Float64}, vcff… ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:20 Reader ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:7 Reader ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:90 readheader!(reader::VariantC… ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:124 _readheader!(reader::Varia… ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:71 fillbuffer!(stream::Buffere… ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1167 readbytes!(s::TranscodingStrea… ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:222 sloweof(stream::Tra… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:624 fillbuffer(stream… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:685 callprocess(stre… ╎ ╎ ╎ ╎ ╎ ╎ 1 @CodecZlib/…:195 process(codec::GzipDecom… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ 15 @VCFTools/…ert.jl:274 convert_gt(t::Type{Float64}, vcff… ╎ ╎ ╎ ╎ 1 @VCFTools/…ats.jl:275 nrecords(vcffile::String) ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:20 Reader ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:7 Reader ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:90 readheader!(reader::Variant… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:124 _readheader!(reader::Vari… ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:71 fillbuffer!(stream::Buffer… ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1174 readbytes!(s::TranscodingStre… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:393 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1020 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1025 _setindex! ╎ ╎ ╎ ╎ 14 @VCFTools/…ats.jl:276 nrecords(vcffile::String) ╎ ╎ ╎ ╎ 14 @VCFTools/…ts.jl:247 countvcflines ╎ ╎ ╎ ╎ 14 @Base/io.jl:1541 countlines ╎ ╎ ╎ ╎ 14 @Base/io.jl:1546 countlines(io::TranscodingStreams.… ╎ ╎ ╎ ╎ ╎ 14 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ 14 @TranscodingStreams/…:222 sloweof(stream::Transco… ╎ ╎ ╎ ╎ ╎ 14 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:622 fillbuffer(stream::Tr… ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:123 makemargin! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:140 makemargin!(buf::Tr… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:291 copyto! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:300 _copyto_impl! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:139 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:623 fillbuffer(stream::Tr… ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:741 readdata!(input::IOS… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ream.jl:43 eof(s::IOStream) 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…eam.jl:262 _eof_nolock ╎ ╎ ╎ ╎ ╎ 12 @TranscodingStreams/…:624 fillbuffer(stream::Tr… ╎ ╎ ╎ ╎ ╎ 12 @TranscodingStreams/…:685 callprocess(stream::… ╎ ╎ ╎ ╎ ╎ ╎ 12 @CodecZlib/…l:195 process(codec::GzipDecompre… 12╎ ╎ ╎ ╎ ╎ ╎ 12 @CodecZlib/…l:127 inflate! ╎ ╎ ╎ ╎ 1 @VCFTools/…ert.jl:275 convert_gt(t::Type{Float64}, vcff… ╎ ╎ ╎ ╎ 1 @VCFTools/…ats.jl:291 nsamples(vcffile::String) ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:20 Reader ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:7 Reader ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:90 readheader!(reader::Variant… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:124 _readheader!(reader::Vari… ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:71 fillbuffer!(stream::Buffer… ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:5 readbytes! 1╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1167 readbytes!(s::TranscodingStre… ╎ ╎ ╎ 1 @VCFTools/…/grm.jl:30 grm(vcffile::String; method::Symbol… ╎ ╎ ╎ 1 @VCFTools/…/grm.jl:123 summarize(x::Matrix{Union{Missing… ╎ ╎ ╎ ╎ 1 @Base/array.jl:621 zeros ╎ ╎ ╎ ╎ 1 @Base/array.jl:623 zeros ╎ ╎ ╎ ╎ 1 @Base/array.jl:626 zeros ╎ ╎ ╎ ╎ 1 @Base/boot.jl:688 Array ╎ ╎ ╎ ╎ 1 @Base/boot.jl:675 Array 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:615 GenericMemory ╎ ╎ ╎ 184 @VCFTools/…/grm.jl:34 grm(vcffile::String; method::Symbol… ╎ ╎ ╎ 1 @VCFTools/…/grm.jl:62 grm!(G::SubArray{Union{Missing, Fl… ╎ ╎ ╎ ╎ 1 @Base/…oadcast.jl:901 materialize! ╎ ╎ ╎ ╎ 1 @Base/…oadcast.jl:904 materialize! ╎ ╎ ╎ ╎ 1 @Base/…adcast.jl:946 copyto! ╎ ╎ ╎ ╎ 1 @Base/…adcast.jl:993 copyto! ╎ ╎ ╎ ╎ 1 @Base/…mdloop.jl:77 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…dcast.jl:994 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…dcast.jl:615 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…cast.jl:619 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…cast.jl:670 _broadcast_getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…cast.jl:694 _getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ast.jl:664 _broadcast_getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1360 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1406 _getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:311 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:963 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1395 _to_linear_index ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:3068 _sub2ind ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:102 axes 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:10 size ╎ ╎ ╎ 92 @VCFTools/…/grm.jl:63 grm!(G::SubArray{Union{Missing, Fl… ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…l:116 * ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…l:119 mul ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:123 _mul ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:270 mul! ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:302 mul! ╎ ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:333 _mul! ╎ ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:348 generic_matmatmul_wrapper! ╎ ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:1115 generic_matmatmul! ╎ ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:1125 _generic_matmatmul!(C::Ma… ╎ ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:1132 __generic_matmatmul! ╎ ╎ ╎ ╎ ╎ ╎ 92 @LinearAlgebra/…:1172 _generic_matmatmul_gene… 15╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…oop.jl:75 macro expansion 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 70 @Base/…oop.jl:77 macro expansion 19╎ ╎ ╎ ╎ ╎ ╎ 70 @LinearAlgebra/…:1173 macro expansion 30╎ ╎ ╎ ╎ ╎ ╎ 30 @Base/…at.jl:497 muladd ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ay.jl:311 getindex ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ay.jl:963 getindex 12╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ls.jl:965 getindex 4╎ ╎ ╎ ╎ ╎ ╎ 9 @LinearAlgebra/…:348 getindex ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:311 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:963 getindex 5╎ ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ls.jl:965 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…oop.jl:84 macro expansion ╎ ╎ ╎ 1 @VCFTools/…/grm.jl:70 grm!(G::SubArray{Union{Missing, Fl… ╎ ╎ ╎ ╎ 1 @VCFTools/…/grm.jl:90 _impute_center_scale! ╎ ╎ ╎ ╎ 1 @VCFTools/…grm.jl:106 _impute_center_scale!(x::SubArra… ╎ ╎ ╎ ╎ 1 @Base/range.jl:925 iterate 1╎ ╎ ╎ ╎ 1 @Base/…motion.jl:637 == ╎ ╎ ╎ 89 @VCFTools/…/grm.jl:72 grm!(G::SubArray{Union{Missing, Fl… ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…l:116 * ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…l:119 mul ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:123 _mul ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:270 mul! ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:302 mul! ╎ ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:333 _mul! ╎ ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:348 generic_matmatmul_wrapper! ╎ ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:1115 generic_matmatmul! ╎ ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:1125 _generic_matmatmul!(C::Ma… ╎ ╎ ╎ ╎ ╎ 89 @LinearAlgebra/…:1132 __generic_matmatmul! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @LinearAlgebra/…:1170 _generic_matmatmul_gene… ╎ ╎ ╎ ╎ ╎ ╎ 88 @LinearAlgebra/…:1172 _generic_matmatmul_gene… 12╎ ╎ ╎ ╎ ╎ ╎ 13 @Base/…oop.jl:75 macro expansion 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ ╎ 75 @Base/…oop.jl:77 macro expansion 19╎ ╎ ╎ ╎ ╎ ╎ 75 @LinearAlgebra/…:1173 macro expansion 27╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…at.jl:497 muladd ╎ ╎ ╎ ╎ ╎ ╎ 20 @Base/…ay.jl:311 getindex ╎ ╎ ╎ ╎ ╎ ╎ 20 @Base/…ay.jl:963 getindex 20╎ ╎ ╎ ╎ ╎ ╎ ╎ 20 @Base/…ls.jl:965 getindex 5╎ ╎ ╎ ╎ ╎ ╎ 9 @LinearAlgebra/…:348 getindex ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:311 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:963 getindex 4╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ls.jl:965 getindex ╎ ╎ ╎ 1 @VCFTools/…/grm.jl:73 grm!(G::SubArray{Union{Missing, Fl… ╎ ╎ ╎ ╎ 1 @Base/…oadcast.jl:901 materialize! ╎ ╎ ╎ ╎ 1 @Base/…oadcast.jl:904 materialize! ╎ ╎ ╎ ╎ 1 @Base/…adcast.jl:946 copyto! ╎ ╎ ╎ ╎ 1 @Base/…adcast.jl:993 copyto! ╎ ╎ ╎ ╎ 1 @Base/…mdloop.jl:77 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…dcast.jl:994 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…ional.jl:774 setindex! ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1031 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1037 _setindex! ╎ ╎ ╎ 1 @LinearAlgebra/…jl:423 eigmin(A::Matrix{Union{Missing, Flo… ╎ ╎ ╎ 1 @LinearAlgebra/…jl:424 eigmin(A::Matrix{Union{Missing, Fl… ╎ ╎ ╎ 1 @LinearAlgebra/…jl:345 eigvals ╎ ╎ ╎ ╎ 1 @LinearAlgebra/…l:345 eigvals(A::Matrix{Union{Missing, … ╎ ╎ ╎ ╎ 1 @LinearAlgebra/…l:310 eigvals! ╎ ╎ ╎ ╎ 1 @LinearAlgebra/…:311 eigvals!(A::Matrix{Float64}; per… ╎ ╎ ╎ ╎ 1 @LinearAlgebra/…:127 eigvals! ╎ ╎ ╎ ╎ 1 @LinearAlgebra/…:133 #eigvals!#258 1╎ ╎ ╎ ╎ ╎ 1 @LinearAlgebra/…:5410 syevr!(jobz::Char, range::Ch… grm | 11 11 8.7s Testing VCFTools tests passed Testing completed after 2663.57s ====================================================================================== 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 1 of 1 signal (10): User defined signal 1 gc_sweep_sysimg at /source/src/staticdata.c:2219 gc_sweep_perm_alloc at /source/src/gc-stock.c:1487 [inlined] _jl_gc_collect at /source/src/gc-stock.c:3210 ijl_gc_collect at /source/src/gc-stock.c:3501 gc at ./gcutils.jl:133 [inlined] temp_cleanup_purge_all at ./file.jl:682 temp_cleanup_atexit at ./file.jl:714 jfptr_temp_cleanup_atexit_53414.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _atexit at ./initdefs.jl:485 jfptr__atexit_69711.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2285 [inlined] ijl_atexit_hook at /source/src/init.c:264 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7426df7f1249) 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) PkgEval terminated after 2713.48s: test duration exceeded the time limit