Package evaluation to test VCFTools on Julia 1.11.7 (58327cce5e*) started at 2025-10-28T22:37:11.414 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.78s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.11/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [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 v1.0.3 [38540f10] + CommonSolve v0.2.4 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.1 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.14.0 [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 v1.2.1 [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 v1.7.1 [2913bbd2] + StatsBase v0.34.7 [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 v1.11.0 [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 v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+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 5.1s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 69.84s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_yYuFjj/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 v0.34.7 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [37e2e46d] LinearAlgebra v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_yYuFjj/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [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 v1.0.3 [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 v0.19.1 [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 v1.14.0 [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 v1.2.1 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [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 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.7 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.1 [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 v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [b27032c2] LibCURL v0.6.4 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.2.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.11.0 [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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling CSV... 21964.7 ms ✓ CSV 1 dependency successfully precompiled in 23 seconds. 29 already precompiled. Precompiling DataFrames... 84532.1 ms ✓ DataFrames 1 dependency successfully precompiled in 85 seconds. 34 already precompiled. Test Summary: | Pass Total Time H-W test | 1 1 2.3s Test Summary: | Pass Total Time openvcf | 4 4 1.5s 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 2.7s ┌ 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: 0:26:52 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 11.307786 seconds (7.69 M allocations: 468.708 MiB, 1.56% gc time, 91.59% compilation time) 0.693244 seconds (2.85 M allocations: 195.158 MiB, 5.19% gc time, 12.22% compilation time) Progress: 0%| | ETA: 0:36:03 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.840024 seconds (4.49 M allocations: 304.101 MiB, 1.75% gc time, 85.78% compilation time) 0.670225 seconds (2.85 M allocations: 195.460 MiB, 3.94% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 19.2s 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 2.1s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.1s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 2.7s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:22:17 Progress: 0%|▏ | ETA: 0:21:33 Progress: 0%|▏ | ETA: 0:21:02 Progress: 0%|▏ | ETA: 0:20:38 Progress: 0%|▏ | ETA: 0:20:24 Progress: 0%|▎ | ETA: 0:20:13 Progress: 1%|▎ | ETA: 0:20:09 Progress: 1%|▎ | ETA: 0:20:06 Progress: 1%|▎ | ETA: 0:20:15 Progress: 1%|▍ | ETA: 0:20:10 Progress: 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| ETA: 22:34:28 Progress: 17%|███████ | ETA: 0:09:43 Progress: 35%|██████████████▌ | ETA: 0:03:44 Progress: 55%|██████████████████████▍ | ETA: 0:01:42 Progress: 74%|██████████████████████████████▎ | ETA: 0:00:44 Progress: 93%|██████████████████████████████████████▎ | ETA: 0:00:09 Progress: 100%|█████████████████████████████████████████| Time: 0:02:05 [ Info: 488 records are matched 263.816795 seconds (2.19 G allocations: 143.692 GiB, 4.70% gc time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:48 Progress: 0%|▏ | ETA: 0:20:42 Progress: 0%|▏ | ETA: 0:20:37 Progress: 0%|▏ | ETA: 0:20:31 Progress: 0%|▏ | ETA: 0:20:09 Progress: 1%|▎ | ETA: 0:19:52 Progress: 1%|▎ | ETA: 0:19:51 Progress: 1%|▎ | ETA: 0:19:49 Progress: 1%|▎ | ETA: 0:19:44 Progress: 1%|▍ | ETA: 0:19:40 Progress: 1%|▍ | ETA: 0:19:31 Progress: 1%|▍ | ETA: 0:19:24 Progress: 1%|▌ | ETA: 0:19:25 Progress: 1%|▌ | ETA: 0:19:25 Progress: 1%|▌ | ETA: 0:19:26 Progress: 1%|▌ | ETA: 0:19:28 Progress: 1%|▋ | ETA: 0:19:29 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ETA: 0:18:27 Progress: 9%|███▉ | ETA: 0:18:26 Progress: 9%|███▉ | ETA: 0:18:25 Progress: 10%|███▉ | ETA: 0:18:24 Progress: 10%|███▉ | ETA: 0:18:23 Progress: 10%|████ | ETA: 0:18:22 Progress: 10%|████ | ETA: 0:18:21 Progress: 10%|████ | ETA: 0:18:20 Progress: 10%|████▏ | ETA: 0:18:20 Progress: 10%|████▏ | ETA: 0:18:19 Progress: 10%|████▏ | ETA: 0:18:18 Progress: 10%|████▏ | ETA: 0:18:17 Progress: 10%|████▎ | ETA: 0:18:16 Progress: 10%|████▎ | ETA: 0:18:15 Progress: 100%|█████████████████████████████████████████| Time: 0:02:06 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 23:09:55 Progress: 17%|███████ | ETA: 0:10:05 Progress: 35%|██████████████▍ | ETA: 0:03:53 Progress: 54%|██████████████████████ | ETA: 0:01:49 Progress: 72%|█████████████████████████████▋ | ETA: 0:00:49 Progress: 93%|██████████████████████████████████████ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:02:08 [ Info: 0 records are matched 272.366608 seconds (2.19 G allocations: 143.692 GiB, 4.68% gc time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 13m25.0s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 23:00:13 Progress: 17%|██████▊ | ETA: 0:10:23 Progress: 34%|█████████████▉ | ETA: 0:04:03 Progress: 52%|█████████████████████▍ | ETA: 0:01:55 Progress: 70%|████████████████████████████▉ | ETA: 0:00:53 Progress: 90%|█████████████████████████████████████ | ETA: 0:00:14 Progress: 100%|█████████████████████████████████████████| Time: 0:02:07 [ Info: 833 records are matched 144.631786 seconds (1.11 G allocations: 72.784 GiB, 4.47% gc time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:19:14 Progress: 17%|██████▉ | ETA: 0:09:49 Progress: 35%|██████████████▎ | ETA: 0:03:47 Progress: 54%|██████████████████████ | ETA: 0:01:45 Progress: 73%|█████████████████████████████▊ | ETA: 0:00:46 Progress: 94%|██████████████████████████████████████▍ | ETA: 0:00:08 Progress: 100%|█████████████████████████████████████████| Time: 0:02:04 [ Info: 493 records are matched 141.671438 seconds (1.11 G allocations: 72.784 GiB, 4.36% gc time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:36:08 Progress: 17%|███████▏ | ETA: 0:09:35 Progress: 36%|██████████████▊ | ETA: 0:03:37 Progress: 55%|██████████████████████▊ | ETA: 0:01:39 Progress: 75%|██████████████████████████████▊ | ETA: 0:00:42 Progress: 97%|███████████████████████████████████████▋ | ETA: 0:00:04 Progress: 100%|█████████████████████████████████████████| Time: 0:02:05 [ Info: 0 records are matched 142.226429 seconds (1.11 G allocations: 72.785 GiB, 4.39% gc time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 7m11.1s 1.730938 seconds (1.27 M allocations: 86.950 MiB, 2.17% gc time, 87.75% compilation time) 1.347779 seconds (1.16 M allocations: 83.630 MiB, 81.79% compilation time) 1.304132 seconds (1.17 M allocations: 82.793 MiB, 3.00% gc time, 84.98% compilation time) 0.945986 seconds (312.97 k allocations: 16.071 MiB, 2.10% gc time, 99.98% compilation time) 0.013643 seconds (10.11 k allocations: 674.188 KiB, 96.41% compilation time) 0.010354 seconds (2.63 k allocations: 242.977 KiB, 96.25% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 11.7s 0.537218 seconds (605.78 k allocations: 54.899 MiB, 64.62% compilation time) 0.215304 seconds (523.79 k allocations: 52.393 MiB, 8.47% gc time, 5.52% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 2.8s Test Summary: | Pass Total Time convert_ds | 5 5 1.3s 0.132103 seconds (524.96 k allocations: 50.415 MiB, 26.40% compilation time) 0.137118 seconds (520.50 k allocations: 50.187 MiB, 22.63% gc time, 8.75% 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 0.085839 seconds (520.44 k allocations: 51.912 MiB, 4.47% gc time) 0.482200 seconds (520.48 k allocations: 51.915 MiB, 79.93% gc time, 2.56% 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 0.187430 seconds (2.07 M allocations: 95.631 MiB, 16.86% gc time) 0.180809 seconds (2.07 M allocations: 95.635 MiB, 7.67% gc time, 5.84% 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 1.8s Test Summary: | Pass Total Time record info | 14 14 8.6s Test Summary: | Pass Total Time write VCF | 3 3 4.7s 1.264559 seconds (4.89 M allocations: 358.428 MiB, 5.70% gc time) 1.045265 seconds (2.83 M allocations: 193.117 MiB, 3.38% gc time) 1.246590 seconds (4.89 M allocations: 358.368 MiB, 3.70% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.1s 1.225810 seconds (612.01 k allocations: 53.363 MiB, 0.95% gc time, 40.37% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.3s Test Summary: | Pass Total Time filter_chr | 4 4 1.7s Progress: 0%|▏ | ETA: 0:22:41 Progress: 1%|▎ | ETA: 0:22:25 Progress: 1%|▌ | ETA: 0:22:28 Progress: 1%|▋ | ETA: 0:22:24 Progress: 2%|▊ | ETA: 0:22:22 Progress: 2%|▉ | ETA: 0:22:17 Progress: 3%|█ | ETA: 0:22:13 Progress: 3%|█▎ | ETA: 0:22:08 Progress: 3%|█▍ | ETA: 0:22:05 Progress: 4%|█▌ | ETA: 0:22:00 Progress: 4%|█▋ | ETA: 0:21:56 Progress: 4%|█▉ | ETA: 0:21:44 Progress: 5%|██ | ETA: 0:21:39 Progress: 5%|██▏ | ETA: 0:21:34 Progress: 6%|██▎ | ETA: 0:21:30 Progress: 6%|██▍ | ETA: 0:21:26 Progress: 6%|██▋ | ETA: 0:21:22 Progress: 7%|██▊ | ETA: 0:21:18 Progress: 7%|██▉ | ETA: 0:21:14 Progress: 7%|███ | ETA: 0:21:11 Progress: 8%|███▏ | ETA: 0:21:07 Progress: 8%|███▎ | ETA: 0:21:03 Progress: 8%|███▌ | ETA: 0:20:57 Progress: 9%|███▋ | ETA: 0:20:53 Progress: 9%|███▊ | 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A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 31 running 1 of 1 signal (10): User defined signal 1 jl_f_memoryrefset at /source/src/builtins.c:1759 _deepcopy_memory_t at ./deepcopy.jl:118 deepcopy_internal at ./deepcopy.jl:99 [inlined] deepcopy_internal at ./deepcopy.jl:137 deepcopy_internal at ./deepcopy.jl:128 deepcopy at ./deepcopy.jl:29 [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:206 [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 [inlined] macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_invoke at /source/src/gf.c:2958 jl_toplevel_eval_flex at /source/src/toplevel.c:934 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2775 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 _include at ./loading.jl:2835 include at ./sysimg.jl:38 unknown function (ip: 0x7a7674900082) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2775 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 _include at ./loading.jl:2835 include at ./sysimg.jl:38 unknown function (ip: 0x7a7674900082) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] exec_options at ./client.jl:289 _start at ./client.jl:524 jfptr__start_73678.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] true_main at /source/src/jlapi.c:900 jl_repl_entrypoint at /source/src/jlapi.c:1059 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7a7675ef7249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) ============================================================== Profile collected. A report will print at the next yield point ============================================================== Progress: 80%|████████████████████████████████▉ | ETA: 0:04:24┌ 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/v1.11/Profile/src/Profile.jl:1240 Overhead ╎ [+additional indent] Count File:Line; Function ========================================================= Thread 1 Task 0x00007a7668ffc010 Total snapshots: 379. Utilization: 100% ╎378 @Base/client.jl:524; _start() ╎ 378 @Base/client.jl:289; exec_options(opts::Base.JLOptions) ╎ 378 @Base/boot.jl:430; eval ╎ 378 @Base/sysimg.jl:38; include(fname::String) ╎ 378 @Base/loading.jl:2835; _include(mapexpr::Function, mod::Module, _pat… ╎ 378 @Base/loading.jl:2775; include_string(mapexpr::typeof(identity), mo… ╎ ╎ 378 @Base/boot.jl:430; eval ╎ ╎ 378 @Base/sysimg.jl:38; include(fname::String) ╎ ╎ 378 @Base/loading.jl:2835; _include(mapexpr::Function, mod::Module, … ╎ ╎ 378 @Base/loading.jl:2775; include_string(mapexpr::typeof(identity)… ╎ ╎ 378 @Base/boot.jl:430; eval ╎ ╎ ╎ 378 …ls/test/aim_test.jl:3; top-level scope ╎ ╎ ╎ 378 @Test/src/Test.jl:1709; macro expansion ╎ ╎ ╎ 378 …s/test/aim_test.jl:19; macro expansion ╎ ╎ ╎ 378 …src/aim_select.jl:26; aim_select ╎ ╎ ╎ 60 …src/aim_select.jl:44; aim_select(vcffile::String, sample… 1╎ ╎ ╎ ╎ 1 @Base/range.jl:0; aim_select(record::VariantCallFormat.R… 1╎ ╎ ╎ ╎ 1 …e/special/log.jl:261; log(x::Float64) ╎ ╎ ╎ ╎ 6 …rc/aim_select.jl:65; aim_select(record::VariantCallForm… ╎ ╎ ╎ ╎ 6 …s/src/gtstats.jl:122; gtstats ╎ ╎ ╎ ╎ 1 …/src/gtstats.jl:125; gtstats(record::VariantCallForma… 1╎ ╎ ╎ ╎ 1 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 4 …/src/gtstats.jl:127; gtstats(record::VariantCallForma… 2╎ ╎ ╎ ╎ 2 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 2 …/src/convert.jl:225; geno_ismissing ╎ ╎ ╎ ╎ 1 …e/essentials.jl:916; getindex 1╎ ╎ ╎ ╎ ╎ 1 …e/essentials.jl:11; length 1╎ ╎ ╎ ╎ 1 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 1 …/src/gtstats.jl:132; gtstats(record::VariantCallForma… 1╎ ╎ ╎ ╎ 1 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 48 …rc/aim_select.jl:74; aim_select(record::VariantCallForm… ╎ ╎ ╎ ╎ 48 @Base/array.jl:2404; findfirst ╎ ╎ ╎ ╎ 46 @Base/array.jl:2353; findnext 7╎ ╎ ╎ ╎ 7 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 39 …se/operators.jl:1144; Fix2 ╎ ╎ ╎ ╎ 39 …se/operators.jl:134; isequal 38╎ ╎ ╎ ╎ ╎ 39 …ings/string.jl:162; == ╎ ╎ ╎ ╎ 2 @Base/array.jl:2354; findnext 2╎ ╎ ╎ ╎ 2 …se/promotion.jl:639; == ╎ ╎ ╎ ╎ 1 …rc/aim_select.jl:76; aim_select(record::VariantCallForm… ╎ ╎ ╎ ╎ 1 …at/src/record.jl:613; findgenokey ╎ ╎ ╎ ╎ 1 @Base/array.jl:2404; findfirst ╎ ╎ ╎ ╎ 1 @Base/array.jl:2353; findnext ╎ ╎ ╎ ╎ 1 …t/src/record.jl:613; #18 ╎ ╎ ╎ ╎ ╎ 1 …/src/record.jl:673; isequaldata 1╎ ╎ ╎ ╎ ╎ 1 …/src/record.jl:677; memcmp ╎ ╎ ╎ ╎ 2 …rc/aim_select.jl:79; aim_select(record::VariantCallForm… 2╎ ╎ ╎ ╎ 2 …se/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 1 …rc/aim_select.jl:99; aim_select(record::VariantCallForm… ╎ ╎ ╎ ╎ 1 …e/special/log.jl:261; log(x::Float64) ╎ ╎ ╎ ╎ 1 …/special/log.jl:289; _log ╎ ╎ ╎ ╎ 1 …/special/log.jl:163; log_proc1 1╎ ╎ ╎ ╎ 1 @Base/float.jl:491; + ╎ ╎ ╎ 318 …src/aim_select.jl:46; aim_select(vcffile::String, sample… ╎ ╎ ╎ ╎ 318 …ase/iterators.jl:206; iterate ╎ ╎ ╎ ╎ 35 …nerics/src/IO.jl:87; iterate ╎ ╎ ╎ ╎ 35 …nerics/src/IO.jl:76; tryread!(reader::VariantCallForm… ╎ ╎ ╎ ╎ 35 …ReaderHelper.jl:142; read!(reader::VariantCallFormat… ╎ ╎ ╎ ╎ 1 …ReaderHelper.jl:156; _read!(reader::VariantCallForm… ╎ ╎ ╎ ╎ ╎ 1 …t/src/record.jl:78; initialize!(record::VariantCal… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2029; empty! ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1207; _deleteend! ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:219; _unsetindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:524; memoryref ╎ ╎ ╎ ╎ 23 …ReaderHelper.jl:165; _read!(reader::VariantCallForm… ╎ ╎ ╎ ╎ ╎ 18 …src/codegen.jl:449; macro expansion ╎ ╎ ╎ ╎ ╎ 4 @Base/array.jl:400; getindex 4╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:579; Array ╎ ╎ ╎ ╎ ╎ 10 @Base/array.jl:1261; push! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1115; _growend! 3╎ ╎ ╎ ╎ ╎ 9 @Base/array.jl:1116; _growend! ╎ ╎ ╎ ╎ ╎ 5 @Base/array.jl:1129; (::Base.var"#133#134"{Vecto… ╎ ╎ ╎ ╎ ╎ 5 …ase/array.jl:1058; array_new_memory 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/boot.jl:516; GenericMemory 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1134; (::Base.var"#133#134"{Vecto… ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:1262; push! 3╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:1001; __safe_setindex! 1╎ ╎ ╎ ╎ ╎ 1 …essentials.jl:917; getindex ╎ ╎ ╎ ╎ ╎ 1 …src/codegen.jl:565; macro expansion ╎ ╎ ╎ ╎ ╎ 1 …src/simdvec.jl:264; & ╎ ╎ ╎ ╎ ╎ 1 …intrinsics.jl:242; and ╎ ╎ ╎ ╎ ╎ 1 …intrinsics.jl:242; and 1╎ ╎ ╎ ╎ ╎ 1 …intrinsics.jl:250; macro expansion 1╎ ╎ ╎ ╎ ╎ 1 …src/codegen.jl:571; macro expansion ╎ ╎ ╎ ╎ ╎ 1 …src/codegen.jl:575; macro expansion ╎ ╎ ╎ ╎ ╎ 1 …src/simdvec.jl:491; all ╎ ╎ ╎ ╎ ╎ 1 …rc/simdvec.jl:486; reduce ╎ ╎ ╎ ╎ ╎ 1 …intrinsics.jl:1050; reduce_and 1╎ ╎ ╎ ╎ ╎ 1 …ntrinsics.jl:1065; macro expansion ╎ ╎ ╎ ╎ ╎ 2 …src/codegen.jl:583; macro expansion ╎ ╎ ╎ ╎ ╎ 1 …/src/memory.jl:56; getindex 1╎ ╎ ╎ ╎ ╎ 1 …/src/memory.jl:49; checkbounds ╎ ╎ ╎ ╎ ╎ 1 …/src/memory.jl:57; getindex 1╎ ╎ ╎ ╎ ╎ 1 …se/pointer.jl:153; unsafe_load ╎ ╎ ╎ ╎ 11 …ReaderHelper.jl:181; _read!(reader::VariantCallForm… ╎ ╎ ╎ ╎ ╎ 11 …dinputstream.jl:61; fillbuffer! ╎ ╎ ╎ ╎ ╎ 11 …inputstream.jl:71; fillbuffer!(stream::BufferedSt… ╎ ╎ ╎ ╎ ╎ 11 …eams/src/io.jl:5; readbytes! ╎ ╎ ╎ ╎ ╎ 1 @Base/io.jl:1151; readbytes!(s::TranscodingStrea… ╎ ╎ ╎ ╎ ╎ 1 …src/stream.jl:213; eof ╎ ╎ ╎ ╎ ╎ ╎ 1 …rc/stream.jl:222; sloweof(stream::Transcoding… ╎ ╎ ╎ ╎ ╎ ╎ 1 …rc/stream.jl:610; fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 …c/stream.jl:624; fillbuffer(stream::Transco… ╎ ╎ ╎ ╎ ╎ ╎ 1 …c/stream.jl:685; callprocess(stream::Trans… ╎ ╎ ╎ ╎ ╎ ╎ 1 …pression.jl:195; process(codec::GzipDecom… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 …src/libz.jl:127; inflate! ╎ ╎ ╎ ╎ ╎ 7 @Base/io.jl:1152; readbytes!(s::TranscodingStrea… ╎ ╎ ╎ ╎ ╎ 7 …src/stream.jl:306; read ╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/io.jl:349; peek ╎ ╎ ╎ ╎ ╎ ╎ 1 …rc/stream.jl:298; peek 1╎ ╎ ╎ ╎ ╎ ╎ 1 …c/stream.jl:209; eof ╎ ╎ ╎ ╎ ╎ ╎ 6 …rc/stream.jl:302; peek 1╎ ╎ ╎ ╎ ╎ ╎ 1 …sentials.jl:916; getindex 5╎ ╎ ╎ ╎ ╎ ╎ 5 …sentials.jl:917; getindex ╎ ╎ ╎ ╎ ╎ 3 @Base/io.jl:1158; readbytes!(s::TranscodingStrea… ╎ ╎ ╎ ╎ ╎ 3 …e/subarray.jl:384; setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 3 …ase/array.jl:987; setindex! ╎ ╎ ╎ ╎ 283 …nerics/src/IO.jl:90; iterate ╎ ╎ ╎ ╎ 283 …t/src/record.jl:309; copy(record::VariantCallFormat.R… ╎ ╎ ╎ ╎ 283 …ase/deepcopy.jl:29; deepcopy ╎ ╎ ╎ ╎ 283 …ase/deepcopy.jl:128; deepcopy_internal(x::Vector{Ve… ╎ ╎ ╎ ╎ ╎ 283 …se/deepcopy.jl:137; deepcopy_internal(x::MemoryRef… ╎ ╎ ╎ ╎ ╎ 283 …se/deepcopy.jl:99; deepcopy_internal 1╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:0; _deepcopy_memory_t(x::Memory, T… 1╎ ╎ ╎ ╎ ╎ 5 …e/deepcopy.jl:106; _deepcopy_memory_t(x::Memory,… 4╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:516; Memory{Vector{UnitRange{Int64… ╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:109; _deepcopy_memory_t(x::Memory,… 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:522; memoryref 38╎ ╎ ╎ ╎ ╎ 38 …e/deepcopy.jl:111; _deepcopy_memory_t(x::Memory,… 10╎ ╎ ╎ ╎ ╎ 10 …e/deepcopy.jl:112; _deepcopy_memory_t(x::Memory,… 39╎ ╎ ╎ ╎ ╎ 39 …e/deepcopy.jl:113; _deepcopy_memory_t(x::Memory,… 5╎ ╎ ╎ ╎ ╎ 162 …e/deepcopy.jl:115; _deepcopy_memory_t(x::Memory,… 1╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:0; deepcopy_internal(x::Vector{Un… 1╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:123; deepcopy_internal(x::Vector{… ╎ ╎ ╎ ╎ ╎ 18 …e/deepcopy.jl:124; deepcopy_internal(x::Vector{… ╎ ╎ ╎ ╎ ╎ 18 …stractdict.jl:19; haskey ╎ ╎ ╎ ╎ ╎ ╎ 18 …se/iddict.jl:182; in 16╎ ╎ ╎ ╎ ╎ ╎ 18 …se/iddict.jl:92; get 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/Base.jl:49; getproperty ╎ ╎ ╎ ╎ ╎ 25 …e/deepcopy.jl:127; deepcopy_internal(x::Vector{… 1╎ ╎ ╎ ╎ ╎ 1 @Base/Base.jl:0; setindex! ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:591; Array 5╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:579; Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:522; memoryref(mem::Memory{Unit… 18╎ ╎ ╎ ╎ ╎ 18 …ase/iddict.jl:86; setindex! 2╎ ╎ ╎ ╎ ╎ 112 …e/deepcopy.jl:128; deepcopy_internal(x::Vector{… 1╎ ╎ ╎ ╎ ╎ 1 @Base/Base.jl:0; _deepcopy_memory_t(x::Memory, … 1╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:0; deepcopy_internal(x::MemoryRe… ╎ ╎ ╎ ╎ ╎ 35 …e/deepcopy.jl:133; deepcopy_internal(x::Memory… ╎ ╎ ╎ ╎ ╎ ╎ 35 …stractdict.jl:19; haskey ╎ ╎ ╎ ╎ ╎ ╎ 35 …se/iddict.jl:182; in 35╎ ╎ ╎ ╎ ╎ ╎ 35 …se/iddict.jl:92; get ╎ ╎ ╎ ╎ ╎ 73 …e/deepcopy.jl:137; deepcopy_internal(x::Memory… ╎ ╎ ╎ ╎ ╎ ╎ 14 …e/deepcopy.jl:96; deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 14 …tractdict.jl:19; haskey ╎ ╎ ╎ ╎ ╎ ╎ 14 …e/iddict.jl:182; in 13╎ ╎ ╎ ╎ ╎ ╎ 13 …e/iddict.jl:92; get 1╎ ╎ ╎ ╎ ╎ ╎ 1 …e/iddict.jl:93; get 4╎ ╎ ╎ ╎ ╎ ╎ 59 …e/deepcopy.jl:99; deepcopy_internal 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/Base.jl:0; _deepcopy_memory_t(x::Memory… 1╎ ╎ ╎ ╎ ╎ ╎ 1 …/deepcopy.jl:102; _deepcopy_memory_t(x::Memo… ╎ ╎ ╎ ╎ ╎ ╎ 1 …/deepcopy.jl:103; _deepcopy_memory_t(x::Memo… 1╎ ╎ ╎ ╎ ╎ ╎ 1 …flection.jl:721; isbitstype 5╎ ╎ ╎ ╎ ╎ ╎ 52 …/deepcopy.jl:104; _deepcopy_memory_t(x::Memo… 18╎ ╎ ╎ ╎ ╎ ╎ 18 …icmemory.jl:170; copy(a::Memory{UnitRange{I… 28╎ ╎ ╎ ╎ ╎ ╎ 28 …e/iddict.jl:86; setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 …e/iddict.jl:87; setindex! ╎ ╎ ╎ ╎ ╎ ╎ 1 …refvalue.jl:59; getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 …ase/Base.jl:49; getproperty 22╎ ╎ ╎ ╎ ╎ 22 …e/deepcopy.jl:117; _deepcopy_memory_t(x::Memory,… 5╎ ╎ ╎ ╎ ╎ 5 …e/deepcopy.jl:118; _deepcopy_memory_t(x::Memory,… ====================================================================================== 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:522 poptask at ./task.jl:1012 wait at ./task.jl:1021 #wait#733 at ./condition.jl:130 wait at ./condition.jl:125 [inlined] wait at ./process.jl:694 wait at ./process.jl:687 unknown function (ip: 0x784c78f62e62) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 subprocess_handler at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2146 #131 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2086 withenv at ./env.jl:265 #118 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1935 with_temp_env at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1793 #116 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1902 #mktempdir#28 at ./file.jl:819 unknown function (ip: 0x784c78f5b5bd) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 mktempdir at ./file.jl:815 mktempdir at ./file.jl:815 [inlined] #sandbox#115 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1849 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1841 unknown function (ip: 0x784c78f4fb3a) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 #test#128 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2067 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [inlined] #test#146 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:460 unknown function (ip: 0x784c78f4f83d) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 #test#77 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 unknown function (ip: 0x784c78f4f20d) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:148 #test#75 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] #test#74 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 unknown function (ip: 0x784c78f4b6a6) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 eval_body at /source/src/interpreter.c:539 eval_body at /source/src/interpreter.c:539 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2775 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 _include at ./loading.jl:2835 include at ./Base.jl:562 jfptr_include_47022.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 exec_options at ./client.jl:316 _start at ./client.jl:524 jfptr__start_73678.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] true_main at /source/src/jlapi.c:900 jl_repl_entrypoint at /source/src/jlapi.c:1059 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x784c7a4da249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) ============================================================== Profile collected. A report will print at the next yield point ============================================================== Progress: 81%|█████████████████████████████████▏ | ETA: 0:04:19┌ 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/v1.11/Profile/src/Profile.jl:1240 Overhead ╎ [+additional indent] Count File:Line; Function ========================================================= Thread 1 Task 0x0000784c6d5fc010 Total snapshots: 44. Utilization: 0% ╎44 @Base/client.jl:524; _start() ╎ 44 @Base/client.jl:316; exec_options(opts::Base.JLOptions) ╎ 44 @Base/Base.jl:562; include(mod::Module, _path::String) ╎ 44 @Base/loading.jl:2835; _include(mapexpr::Function, mod::Module, _path:… ╎ 44 @Base/loading.jl:2775; include_string(mapexpr::typeof(identity), mod:… ╎ 44 @Base/boot.jl:430; eval ╎ ╎ 44 @Pkg/src/API.jl:146; kwcall(::@NamedTuple{julia_args::Cmd}, ::typeo… ╎ ╎ 44 @Pkg/src/API.jl:146; #test#74 ╎ ╎ 44 @Pkg/src/API.jl:147; test ╎ ╎ 44 @Pkg/src/API.jl:147; #test#75 ╎ ╎ 44 @Pkg/src/API.jl:148; kwcall(::@NamedTuple{julia_args::Cmd}, ::t… ╎ ╎ ╎ 44 @Pkg/src/API.jl:159; test(pkgs::Vector{Pkg.Types.PackageSpec};… ╎ ╎ ╎ 44 @Pkg/src/API.jl:460; kwcall(::@NamedTuple{julia_args::Cmd, io… ╎ ╎ ╎ 44 @Pkg/src/API.jl:481; test(ctx::Pkg.Types.Context, pkgs::Vect… ╎ ╎ ╎ 44 …src/Operations.jl:2011; test ╎ ╎ ╎ 44 …src/Operations.jl:2067; test(ctx::Pkg.Types.Context, pkgs… ╎ ╎ ╎ ╎ 44 …rc/Operations.jl:1841; kwcall(::@NamedTuple{preferences:… ╎ ╎ ╎ ╎ 44 …rc/Operations.jl:1849; #sandbox#115 ╎ ╎ ╎ ╎ 44 @Base/file.jl:815; mktempdir ╎ ╎ ╎ ╎ 44 @Base/file.jl:815; mktempdir(fn::Function, parent::Str… ╎ ╎ ╎ ╎ 44 @Base/file.jl:819; mktempdir(fn::Pkg.Operations.var"#… ╎ ╎ ╎ ╎ ╎ 44 …/Operations.jl:1902; (::Pkg.Operations.var"#116#121… ╎ ╎ ╎ ╎ ╎ 44 …/Operations.jl:1793; with_temp_env(fn::Pkg.Operati… ╎ ╎ ╎ ╎ ╎ 44 …Operations.jl:1935; (::Pkg.Operations.var"#118#12… ╎ ╎ ╎ ╎ ╎ 44 @Base/env.jl:265; withenv(::Pkg.Operations.var"#1… ╎ ╎ ╎ ╎ ╎ 44 …Operations.jl:2086; (::Pkg.Operations.var"#131#… ╎ ╎ ╎ ╎ ╎ ╎ 44 …perations.jl:2146; subprocess_handler(cmd::Cmd… ╎ ╎ ╎ ╎ ╎ ╎ 44 …e/process.jl:687; wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 44 …e/process.jl:694; wait(x::Base.Process, sync… ╎ ╎ ╎ ╎ ╎ ╎ 44 …ondition.jl:125; wait ╎ ╎ ╎ ╎ ╎ ╎ 44 …ondition.jl:130; wait(c::Base.GenericCondi… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 44 …ase/task.jl:1021; wait() 43╎ ╎ ╎ ╎ ╎ ╎ ╎ 44 …ase/task.jl:1012; poptask(W::Base.Intrus… [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:522 [31] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 int64hash at /source/src/support/hashing.c:35 immut_id_ at /source/src/builtins.c:413 ijl_object_id_ at /source/src/builtins.c:481 [inlined] jl_table_peek_bp at /source/src/iddict.c:118 [inlined] ijl_eqtable_get at /source/src/iddict.c:157 get at ./iddict.jl:92 [inlined] in at ./iddict.jl:182 [inlined] haskey at ./abstractdict.jl:19 [inlined] deepcopy_internal at ./deepcopy.jl:133 deepcopy_internal at ./deepcopy.jl:128 unknown function (ip: 0x7a76749ac0f6) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 _deepcopy_memory_t at ./deepcopy.jl:115 deepcopy_internal at ./deepcopy.jl:99 [inlined] deepcopy_internal at ./deepcopy.jl:137 deepcopy_internal at ./deepcopy.jl:128 deepcopy at ./deepcopy.jl:29 [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:206 [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 [inlined] macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_invoke at /source/src/gf.c:2958 jl_toplevel_eval_flex at /source/src/toplevel.c:934 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 poptask at ./task.jl:1012 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2775 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 wait at ./task.jl:1021 _include at ./loading.jl:2835 include at ./sysimg.jl:38 unknown function (ip: 0x7a7674900082) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 #wait#733 at ./condition.jl:130 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 wait at ./condition.jl:125 [inlined] _trywait at ./asyncevent.jl:145 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2775 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 profile_printing_listener at ./Base.jl:582 _include at ./loading.jl:2835 include at ./sysimg.jl:38 unknown function (ip: 0x7a7674900082) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 #1192 at ./Base.jl:622 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 jfptr_YY.1192_76252.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] start_task at /source/src/task.c:1202 unknown function (ip: (nil)) Allocations: 19738407 (Pool: 19737674; Big: 733); GC: 18 eval at ./boot.jl:430 [inlined] exec_options at ./client.jl:289 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") _start at ./client.jl:524 error at ./error.jl:35 jfptr__start_73678.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] #schedule#763 at ./task.jl:884 true_main at /source/src/jlapi.c:900 jl_repl_entrypoint at /source/src/jlapi.c:1059 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7a7675ef7249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) Allocations: 18554703538 (Pool: 18554687453; Big: 16085); GC: 34082 schedule at ./task.jl:876 [inlined] uv_writecb_task at ./stream.jl:1200 jfptr_uv_writecb_task_67129.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jlcapi_uv_writecb_task_67593.1 at /opt/julia/lib/julia/sys.so (unknown line) uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926 uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227 uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824 uv_run at /workspace/srcdir/libuv/src/unix/core.c:420 ijl_task_get_next at /source/src/scheduler.c:522 poptask at ./task.jl:1012 wait at ./task.jl:1021 uv_write at ./stream.jl:1081 unsafe_write at ./stream.jl:1154 write at ./strings/io.jl:248 [inlined] print at ./strings/io.jl:250 jfptr_print_48479.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 showerror at ./errorshow.jl:152 unknown function (ip: 0x784c78f6ff86) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 _atexit at ./initdefs.jl:454 jfptr__atexit_69637.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] ijl_atexit_hook at /source/src/init.c:271 jl_exit_thread0_cb at /source/src/signals-unix.c:517 PkgEval terminated after 2723.68s: test duration exceeded the time limit