Package evaluation of VCFTools on Julia 1.13.0-DEV.783 (b4a6288a38*) started at 2025-06-26T23:19:53.987 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.29s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 ⌅ [67c07d97] + Automa v0.8.4 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [34da2185] + Compat v4.16.0 [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 3.95s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 33.68s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_jeBAHX/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_jeBAHX/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 v4.16.0 [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 v3.5.0+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... Precompiling packages... 34848.7 ms ✓ CSV 1 dependency successfully precompiled in 35 seconds. 38 already precompiled. Precompiling packages... 89339.7 ms ✓ DataFrames 1 dependency successfully precompiled in 90 seconds. 34 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 3.9s Test Summary: | Pass Total Time openvcf | 4 4 2.2s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.4s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.5s ┌ 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: 0:25:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 14.530814 seconds (11.11 M allocations: 681.594 MiB, 1.73% gc time, 92.04% compilation time: 20% of which was recompilation) 1.181814 seconds (2.87 M allocations: 195.748 MiB, 4.96% gc time, 7.19% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:22:45 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 3.201207 seconds (4.42 M allocations: 300.009 MiB, 2.00% gc time, 63.97% compilation time) 1.144582 seconds (2.85 M allocations: 195.408 MiB, 2.87% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 24.1s Test Summary: | Pass Total Time get sampleID | 4 4 0.0s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.8s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 5.1s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:38 Progress: 0%|▏ | ETA: 0:18:08 Progress: 0%|▏ | ETA: 0:18:00 Progress: 0%|▏ | ETA: 0:17:54 Progress: 0%|▎ | ETA: 0:17:49 Progress: 1%|▎ | ETA: 0:17:47 Progress: 1%|▎ | ETA: 0:17:52 Progress: 1%|▎ | ETA: 0:17:50 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time, 0.37% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:11 Progress: 0%|▏ | ETA: 0:18:36 Progress: 0%|▏ | ETA: 0:18:14 Progress: 0%|▏ | ETA: 0:17:57 Progress: 0%|▎ | ETA: 0:17:54 Progress: 1%|▎ | ETA: 0:17:55 Progress: 1%|▎ | ETA: 0:17:51 Progress: 1%|▎ | ETA: 0:17:48 Progress: 1%|▍ | ETA: 0:17:45 Progress: 1%|▍ | ETA: 0:17:44 Progress: 1%|▍ | ETA: 0:17:46 Progress: 1%|▌ | ETA: 0:17:47 Progress: 1%|▌ | ETA: 0:17:47 Progress: 1%|▌ | ETA: 0:17:46 Progress: 1%|▋ | ETA: 0:17:43 Progress: 1%|▋ | ETA: 0:17:41 Progress: 2%|▋ | ETA: 0:17:35 Progress: 2%|▊ | ETA: 0:17:31 Progress: 2%|▊ | ETA: 0:17:29 Progress: 2%|▊ | ETA: 0:17:28 Progress: 2%|▉ | ETA: 0:17:22 Progress: 2%|▉ | ETA: 0:17:20 Progress: 2%|▉ | ETA: 0:17:16 Progress: 2%|█ | ETA: 0:17:13 Progress: 2%|█ | ETA: 0:17:12 Progress: 2%|█ | ETA: 0:17:11 Progress: 3%|█ | ETA: 0:17:09 Progress: 3%|█▏ | ETA: 0:17:09 Progress: 3%|█▏ | ETA: 0:17:08 Progress: 3%|█▏ | ETA: 0:17:06 Progress: 3%|█▎ | ETA: 0:17:05 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9%|███▊ | ETA: 0:15:47 Progress: 9%|███▊ | ETA: 0:15:46 Progress: 9%|███▉ | ETA: 0:15:46 Progress: 9%|███▉ | ETA: 0:15:45 Progress: 10%|███▉ | ETA: 0:15:45 Progress: 10%|████ | ETA: 0:15:44 Progress: 10%|████ | ETA: 0:15:43 Progress: 10%|████ | ETA: 0:15:42 Progress: 10%|████▏ | ETA: 0:15:41 Progress: 10%|████▏ | ETA: 0:15:40 Progress: 10%|████▏ | ETA: 0:15:39 Progress: 10%|████▏ | ETA: 0:15:38 Progress: 10%|████▎ | ETA: 0:15:37 Progress: 100%|█████████████████████████████████████████| Time: 0:01:47 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:19:08 Progress: 26%|██████████▌ | ETA: 0:05:02 Progress: 51%|████████████████████▉ | ETA: 0:01:41 Progress: 76%|███████████████████████████████ | ETA: 0:00:34 Progress: 99%|████████████████████████████████████████▊| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:01:46 [ Info: 0 records are matched 226.750973 seconds (2.19 G allocations: 143.726 GiB, 6.78% gc time, 0.38% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m52.3s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:21:40 Progress: 17%|███████▏ | ETA: 0:08:39 Progress: 36%|██████████████▊ | ETA: 0:03:16 Progress: 57%|███████████████████████▎ | ETA: 0:01:25 Progress: 77%|███████████████████████████████▊ | ETA: 0:00:33 Progress: 98%|████████████████████████████████████████▍| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: 833 records are matched 123.301816 seconds (1.11 G allocations: 72.817 GiB, 6.58% gc time, 0.42% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:53:57 Progress: 20%|████████ | ETA: 0:07:18 Progress: 39%|████████████████▏ | ETA: 0:02:46 Progress: 62%|█████████████████████████▍ | ETA: 0:01:07 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 493 records are matched 121.977182 seconds (1.11 G allocations: 72.817 GiB, 6.44% gc time, 0.44% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:42:16 Progress: 20%|████████▏ | ETA: 0:07:08 Progress: 40%|████████████████▌ | ETA: 0:02:38 Progress: 62%|█████████████████████████▌ | ETA: 0:01:06 Progress: 87%|███████████████████████████████████▋ | ETA: 0:00:16 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 0 records are matched 120.208430 seconds (1.11 G allocations: 72.816 GiB, 6.11% gc time, 0.48% compilation time: <1% of which was recompilation) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m07.9s 1.113387 seconds (1.35 M allocations: 93.684 MiB, 3.77% gc time, 85.13% compilation time) 0.949646 seconds (1.22 M allocations: 88.659 MiB, 2.95% gc time, 81.44% compilation time) 0.896008 seconds (1.23 M allocations: 87.936 MiB, 2.08% gc time, 83.33% compilation time) 0.402824 seconds (221.21 k allocations: 12.131 MiB, 99.96% compilation time) 0.009361 seconds (6.31 k allocations: 485.336 KiB, 95.84% compilation time) 0.008597 seconds (2.67 k allocations: 248.242 KiB, 96.15% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 8.9s 0.795075 seconds (994.70 k allocations: 75.908 MiB, 3.93% gc time, 82.12% compilation time) 0.736536 seconds (896.22 k allocations: 72.708 MiB, 2.97% gc time, 87.09% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.4s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.124736 seconds (525.77 k allocations: 50.465 MiB, 15.95% gc time, 25.66% compilation time) 0.624681 seconds (661.49 k allocations: 58.144 MiB, 2.24% gc time, 86.00% 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 0.071725 seconds (520.43 k allocations: 51.916 MiB, 15.53% gc time) 0.533215 seconds (596.82 k allocations: 56.238 MiB, 2.46% gc time, 86.27% 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 0.137040 seconds (1.56 M allocations: 81.839 MiB, 9.49% gc time, 6.61% compilation time) 0.635598 seconds (1.72 M allocations: 90.800 MiB, 11.32% gc time, 72.03% 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 6.9s Test Summary: | Pass Total Time record info | 14 14 8.0s Test Summary: | Pass Total Time write VCF | 3 3 5.2s 2.836190 seconds (5.29 M allocations: 379.800 MiB, 2.73% gc time, 41.01% compilation time) 1.802495 seconds (2.86 M allocations: 195.091 MiB, 2.45% gc time, 12.15% compilation time) 1.648907 seconds (4.89 M allocations: 358.188 MiB, 3.66% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 8.9s 1.695074 seconds (629.28 k allocations: 54.757 MiB, 0.90% gc time, 27.97% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.5s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▏ | ETA: 0:22:06 Progress: 1%|▍ | ETA: 0:20:56 Progress: 1%|▌ | ETA: 0:20:25 Progress: 2%|▋ | ETA: 0:19:51 Progress: 2%|▉ | ETA: 0:19:46 Progress: 3%|█ | ETA: 0:19:47 Progress: 3%|█▎ | ETA: 0:19:47 Progress: 3%|█▍ | ETA: 0:19:48 Progress: 4%|█▌ | ETA: 0:19:49 Progress: 4%|█▋ | ETA: 0:19:46 Progress: 4%|█▉ | ETA: 0:19:43 Progress: 5%|██ | ETA: 0:19:38 Progress: 5%|██▏ | ETA: 0:19:31 Progress: 6%|██▍ | ETA: 0:19:24 Progress: 6%|██▌ | ETA: 0:19:19 Progress: 7%|██▋ | ETA: 0:19:14 Progress: 7%|██▉ | ETA: 0:19:11 Progress: 7%|███ | ETA: 0:19:09 Progress: 8%|███▏ | ETA: 0:19:05 Progress: 8%|███▍ | ETA: 0:19:01 Progress: 9%|███▌ | ETA: 0:18:51 Progress: 9%|███▊ | ETA: 0:18:46 Progress: 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====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 19 running 1 of 1 signal (10): User defined signal 1 gc_alloc_map_set at /source/src/gc-stock.h:302 [inlined] jl_gc_alloc_page at /source/src/gc-pages.c:113 gc_add_page at /source/src/gc-stock.c:702 jl_gc_small_alloc_inner at /source/src/gc-stock.c:763 jl_gc_small_alloc_noinline at /source/src/gc-stock.c:783 [inlined] jl_gc_alloc_ at /source/src/gc-stock.c:797 jl_alloc_genericmemory_unchecked at /source/src/genericmemory.c:41 GenericMemory at ./boot.jl:588 [inlined] copy at ./genericmemory.jl:179 unknown function (ip: 0x7ada85ef28a2) at (unknown file) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _deepcopy_memory_t at ./deepcopy.jl:109 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_invoke at /source/src/gf.c:3699 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x7ada85ef22c6) at (unknown file) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _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: 0x7ada677520a6) at (unknown file) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 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:3692 [inlined] ijl_invoke at /source/src/gf.c:3699 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:2846 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_28212.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [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:2846 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_28212.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [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_72738.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] true_main at /source/src/jlapi.c:964 jl_repl_entrypoint at /source/src/jlapi.c:1132 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7ada871af249) 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: 99%|████████████████████████████████████████▍| ETA: 0:00:18┌ 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 0x00007ada6d200010 Total snapshots: 1. Utilization: 100% ╎1 @Base/client.jl:557 _start() ╎ 1 @Base/client.jl:290 exec_options(opts::Base.JLOptions) ╎ 1 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 1 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 1 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::Strin… ╎ 1 @Base/loading.jl:2906 _include(mapexpr::Function, mod::Module, _path:… ╎ ╎ 1 @Base/loading.jl:2846 include_string(mapexpr::typeof(identity), mod:… ╎ ╎ 1 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 1 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 1 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::… ╎ ╎ 1 @Base/loading.jl:2906 _include(mapexpr::Function, mod::Module, _… ╎ ╎ ╎ 1 @Base/loading.jl:2846 include_string(mapexpr::typeof(identity),… ╎ ╎ ╎ 1 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 1 @VCFTools/…m_test.jl:3 top-level scope ╎ ╎ ╎ 1 @Test/src/Test.jl:1855 macro expansion ╎ ╎ ╎ 1 @VCFTools/…_test.jl:19 macro expansion ╎ ╎ ╎ ╎ 1 @VCFTools/…elect.jl:26 aim_select(vcffile::String, sampleI… ╎ ╎ ╎ ╎ 1 @VCFTools/…lect.jl:46 aim_select(vcffile::String, sampleI… ╎ ╎ ╎ ╎ 1 @Base/iterators.jl:197 iterate ╎ ╎ ╎ ╎ 1 @BioGenerics/…O.jl:87 iterate ╎ ╎ ╎ ╎ 1 @BioGenerics/….jl:76 tryread!(reader::VariantCallForma… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:147 read!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:185 _read!(reader::VariantCallF… ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:71 fillbuffer! ╎ ╎ ╎ ╎ ╎ 1 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:387 readbytes!(stream::Tra… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:201 eof(stream::Transcodi… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:582 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:596 fillbuffer(stream::… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:656 callprocess(stream… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @CodecZlib/…:195 process(codec::GzipDecompr… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @CodecZlib/…:127 inflate! ====================================================================================== 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_64784.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [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 0x000079fdc3202860 Total snapshots: 481. Utilization: 0% ╎481 @Base/task.jl:1150 wait_forever() 480╎ 481 @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 [19] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 jl_is_genericmemoryref_type at /source/src/julia.h:1745 [inlined] jl_is_genericmemoryref at /source/src/julia.h:1752 [inlined] jl_f_memoryref_isassigned at /source/src/builtins.c:1869 _deepcopy_memory_t at ./deepcopy.jl:117 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: 0x7ada677520a6) at (unknown file) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 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:3692 [inlined] ijl_invoke at /source/src/gf.c:3699 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 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 eval at ./boot.jl:489 wait_forever at ./task.jl:1150 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _include at ./loading.jl:2906 jfptr_wait_forever_64784.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 18634561 (Pool: 18634078; Big: 483); GC: 16 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_28212.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [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:2846 _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_28212.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [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_72738.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3692 [inlined] ijl_apply_generic at /source/src/gf.c:3892 jl_apply at /source/src/julia.h:2343 [inlined] true_main at /source/src/jlapi.c:964 jl_repl_entrypoint at /source/src/jlapi.c:1132 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7ada871af249) 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: 20502536281 (Pool: 20502520722; Big: 15559); GC: 36713 PkgEval terminated after 2724.35s: test duration exceeded the time limit