Package evaluation of VCFTools on Julia 1.12.0-rc3 (7522b24014*) started at 2025-10-01T19:54:15.075 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.36s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed SIMD ──────────────────── v3.7.1 Installed IrrationalConstants ───── v0.2.4 Installed Rmath ─────────────────── v0.8.0 Installed StatsFuns ─────────────── v1.5.0 Installed HypergeometricFunctions ─ v0.3.28 Installed BioGenerics ───────────── v0.1.5 Installed Preferences ───────────── v1.5.0 Installed Accessors ─────────────── v0.1.42 Installed PtrArrays ─────────────── v1.3.0 Installed PDMats ────────────────── v0.11.35 Installed JLLWrappers ───────────── v1.7.1 Installed ProgressMeter ─────────── v1.11.0 Installed DataAPI ───────────────── v1.16.0 Installed SpecialFunctions ──────── v2.5.1 Installed Roots ─────────────────── v2.2.10 Installed PrecompileTools ───────── v1.3.3 Installed ConstructionBase ──────── v1.6.0 Installed OrderedCollections ────── v1.8.1 Installed DelimitedFiles ────────── v1.9.1 Installed HypothesisTests ───────── v0.11.5 Installed TranscodingStreams ────── v0.11.3 Installed QuadGK ────────────────── v2.11.2 Installed Combinatorics ─────────── v1.0.3 Installed BGZFStreams ───────────── v0.3.2 Installed FillArrays ────────────── v1.14.0 Installed Rmath_jll ─────────────── v0.5.1+0 Installed Reexport ──────────────── v1.2.2 Installed Statistics ────────────── v1.11.1 Installed DataStructures ────────── v0.19.1 Installed LogExpFunctions ───────── v0.3.29 Installed AliasTables ───────────── v1.1.3 Installed BufferedStreams ───────── v1.2.2 Installed MacroTools ────────────── v0.5.16 Installed VariantCallFormat ─────── v0.5.7 Installed VCFTools ──────────────── v0.2.10 Installed StatsAPI ──────────────── v1.7.1 Installed CompositionsBase ──────── v0.1.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed InverseFunctions ──────── v0.1.17 Installed Distributions ─────────── v0.25.120 Installed CodecZlib ─────────────── v0.7.8 Installed CommonSolve ───────────── v0.2.4 Installed Automa ────────────────── v1.1.0 Installed Missings ──────────────── v1.2.0 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed StatsBase ─────────────── v0.34.6 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.12/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.12/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 v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.14.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [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 v0.8.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.1 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.7 [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 v1.12.0 [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 [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 v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+1 Installation completed after 10.32s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4391.4 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 438.6s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_4jarE3/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.6 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.7 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_4jarE3/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 v1.8.0 [864edb3b] DataStructures v0.19.1 [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 v1.14.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [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 v0.11.35 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.0.11 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.6 [4c63d2b9] StatsFuns v1.5.0 [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 v0.5.7 [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 [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 [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 v1.12.0 [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 v8.11.1+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+1 [8e850ede] nghttp2_jll v1.64.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.7s Test Summary: | Pass Total Time openvcf | 4 4 2.7s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.4s ┌ 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: 0:40:08 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 15.451756 seconds (12.00 M allocations: 737.053 MiB, 4.43% gc time, 96.13% compilation time: 20% of which was recompilation) 0.497983 seconds (2.87 M allocations: 195.822 MiB, 13.21% gc time, 17.18% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:30:25 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.199721 seconds (4.83 M allocations: 323.512 MiB, 2.37% gc time, 85.87% compilation time) 0.460127 seconds (2.85 M allocations: 195.431 MiB, 5.05% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.4s 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 1.9s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.1s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.0s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 5.9s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:55 Progress: 0%|▏ | ETA: 0:18:53 Progress: 0%|▏ | ETA: 0:18:15 Progress: 0%|▏ | ETA: 0:17:52 Progress: 0%|▎ | ETA: 0:17:49 Progress: 1%|▎ | ETA: 0:17:39 Progress: 1%|▎ | ETA: 0:17:32 Progress: 1%|▍ | ETA: 0:17:27 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0.36% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:22:40 Progress: 0%|▏ | ETA: 0:20:46 Progress: 0%|▏ | ETA: 0:20:07 Progress: 0%|▏ | ETA: 0:19:44 Progress: 0%|▏ | ETA: 0:19:32 Progress: 1%|▎ | ETA: 0:19:11 Progress: 1%|▎ | ETA: 0:19:06 Progress: 1%|▎ | ETA: 0:19:01 Progress: 1%|▍ | ETA: 0:18:57 Progress: 1%|▍ | ETA: 0:18:56 Progress: 1%|▍ | ETA: 0:18:53 Progress: 1%|▍ | ETA: 0:18:51 Progress: 1%|▌ | ETA: 0:18:47 Progress: 1%|▌ | ETA: 0:18:44 Progress: 1%|▌ | ETA: 0:18:41 Progress: 1%|▋ | ETA: 0:18:40 Progress: 2%|▋ | ETA: 0:18:37 Progress: 2%|▋ | ETA: 0:18:34 Progress: 2%|▊ | ETA: 0:18:32 Progress: 2%|▊ | ETA: 0:18:30 Progress: 2%|▊ | ETA: 0:18:28 Progress: 2%|▊ | ETA: 0:18:26 Progress: 2%|▉ | ETA: 0:18:25 Progress: 2%|▉ | ETA: 0:18:24 Progress: 2%|▉ | ETA: 0:18:24 Progress: 2%|█ | ETA: 0:18:22 Progress: 2%|█ | ETA: 0:18:21 Progress: 3%|█ | ETA: 0:18:20 Progress: 3%|█ | ETA: 0:18:19 Progress: 3%|█▏ | ETA: 0:18:18 Progress: 3%|█▏ | ETA: 0:18:16 Progress: 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0:15:53 Progress: 9%|███▊ | ETA: 0:15:52 Progress: 9%|███▉ | ETA: 0:15:51 Progress: 9%|███▉ | ETA: 0:15:50 Progress: 10%|███▉ | ETA: 0:15:49 Progress: 10%|███▉ | ETA: 0:15:48 Progress: 10%|████ | ETA: 0:15:47 Progress: 10%|████ | ETA: 0:15:46 Progress: 10%|████ | ETA: 0:15:45 Progress: 10%|████▏ | ETA: 0:15:43 Progress: 10%|████▏ | ETA: 0:15:43 Progress: 10%|████▏ | ETA: 0:15:42 Progress: 10%|████▎ | ETA: 0:15:41 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:49:54 Progress: 20%|████████▏ | ETA: 0:07:12 Progress: 40%|████████████████▌ | ETA: 0:02:40 Progress: 61%|█████████████████████████▏ | ETA: 0:01:08 Progress: 83%|██████████████████████████████████▎ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 0 records are matched 238.344994 seconds (2.19 G allocations: 143.726 GiB, 5.89% gc time, 0.42% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m14.2s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:48:52 Progress: 19%|███████▉ | ETA: 0:07:28 Progress: 39%|███████████████▉ | ETA: 0:02:50 Progress: 60%|████████████████████████▋ | ETA: 0:01:12 Progress: 82%|█████████████████████████████████▋ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 833 records are matched 128.254943 seconds (1.11 G allocations: 72.817 GiB, 5.51% gc time, 0.44% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:47:54 Progress: 19%|████████ | ETA: 0:07:22 Progress: 39%|████████████████ | ETA: 0:02:47 Progress: 61%|█████████████████████████ | ETA: 0:01:09 Progress: 84%|██████████████████████████████████▍ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 493 records are matched 127.989271 seconds (1.11 G allocations: 72.817 GiB, 5.45% gc time, 0.45% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 19:47:51 Progress: 20%|████████▍ | ETA: 0:06:56 Progress: 41%|████████████████▉ | ETA: 0:02:33 Progress: 64%|██████████████████████████▏ | ETA: 0:01:01 Progress: 87%|███████████████████████████████████▋ | ETA: 0:00:16 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 0 records are matched 128.025856 seconds (1.11 G allocations: 72.816 GiB, 5.39% gc time, 0.51% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m26.6s 1.405295 seconds (1.41 M allocations: 96.610 MiB, 3.55% gc time, 85.53% compilation time) 1.215393 seconds (1.29 M allocations: 92.245 MiB, 2.82% gc time, 76.98% compilation time) 1.122174 seconds (1.29 M allocations: 91.260 MiB, 81.86% compilation time) 0.506403 seconds (236.93 k allocations: 13.101 MiB, 4.04% gc time, 99.97% compilation time) 0.012537 seconds (6.82 k allocations: 512.977 KiB, 96.84% compilation time) 0.010857 seconds (2.73 k allocations: 252.555 KiB, 96.82% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.8s 0.938418 seconds (1.05 M allocations: 79.357 MiB, 5.45% gc time, 74.14% compilation time) 0.768429 seconds (935.68 k allocations: 74.974 MiB, 2.92% gc time, 70.44% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.5s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.133866 seconds (526.13 k allocations: 50.495 MiB, 9.61% gc time, 27.57% compilation time) 0.768537 seconds (671.35 k allocations: 58.512 MiB, 1.52% gc time, 86.78% 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 0.082913 seconds (520.43 k allocations: 51.916 MiB) 0.414594 seconds (606.07 k allocations: 56.855 MiB, 72.83% 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 0.195452 seconds (1.56 M allocations: 81.843 MiB, 16.27% gc time, 4.73% compilation time) 0.715250 seconds (1.74 M allocations: 92.027 MiB, 82.71% 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 6.2s Test Summary: | Pass Total Time record info | 14 14 5.6s Test Summary: | Pass Total Time write VCF | 3 3 3.7s 2.202699 seconds (5.31 M allocations: 381.327 MiB, 2.88% gc time, 55.56% compilation time) 1.019336 seconds (2.86 M allocations: 194.865 MiB, 3.54% gc time, 21.78% compilation time) 0.968260 seconds (4.89 M allocations: 358.319 MiB, 5.52% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.2s 1.083222 seconds (626.00 k allocations: 54.411 MiB, 1.25% gc time, 48.24% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.0s Test Summary: | Pass Total Time filter_chr | 4 4 1.6s Progress: 0%|▏ | ETA: 0:23:20 Progress: 1%|▍ | ETA: 0:21:33 Progress: 1%|▌ | ETA: 0:21:06 Progress: 2%|▋ | ETA: 0:20:45 Progress: 2%|▉ | ETA: 0:20:26 Progress: 2%|█ | ETA: 0:20:18 Progress: 3%|█▏ | ETA: 0:20:13 Progress: 3%|█▍ | ETA: 0:20:10 Progress: 4%|█▌ | ETA: 0:20:06 Progress: 4%|█▋ | ETA: 0:20:01 Progress: 4%|█▉ | ETA: 0:19:56 Progress: 5%|██ | ETA: 0:19:50 Progress: 5%|██▏ | ETA: 0:19:43 Progress: 6%|██▍ | ETA: 0:19:37 Progress: 6%|██▌ | ETA: 0:19:31 Progress: 6%|██▋ | ETA: 0:19:25 Progress: 7%|██▉ | ETA: 0:19:22 Progress: 7%|███ | ETA: 0:19:17 Progress: 8%|███▏ | ETA: 0:19:14 Progress: 8%|███▎ | ETA: 0:19:08 Progress: 8%|███▌ | ETA: 0:19:02 Progress: 9%|███▋ | ETA: 0:18:57 Progress: 9%|███▊ | ETA: 0:18:52 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A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 431 running 1 of 1 signal (10): User defined signal 1 #_growend!##0 at ./array.jl:1156 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 read! at /home/pkgeval/.julia/packages/VariantCallFormat/DDn3I/src/ReaderHelper.jl:142 tryread! at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:76 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:87 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x7d967b42ac36) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_invoke at /source/src/gf.c:4017 jl_toplevel_eval_flex at /source/src/toplevel.c:1024 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2903 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_91637.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2903 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_91637.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 exec_options at ./client.jl:283 _start at ./client.jl:550 jfptr__start_97682.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7d96aa0c3249) 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: 75%|██████████████████████████████▉ | ETA: 0:05:00 ====================================================================================== 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 poptask at ./task.jl:1187 wait at ./task.jl:1199 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] wait at ./process.jl:694 wait at ./process.jl:687 jfptr_wait_91376.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 subprocess_handler at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2445 unknown function (ip: 0x7fd56c19cc73) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 #204 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2385 withenv at ./env.jl:265 #189 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2204 with_temp_env at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2062 #185 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2171 #mktempdir#21 at ./file.jl:899 unknown function (ip: 0x7fd56c194b7c) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 mktempdir at ./file.jl:895 mktempdir at ./file.jl:895 #sandbox#181 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2118 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2110 unknown function (ip: 0x7fd56c1881c9) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 #test#192 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2370 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2280 [inlined] #test#170 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:483 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:462 unknown function (ip: 0x7fd56c187711) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 #test#84 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 unknown function (ip: 0x7fd56c186c10) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:153 #test#82 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] #test#81 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 unknown function (ip: 0x7fd56c17cb5f) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2903 include at ./Base.jl:306 exec_options at ./client.jl:317 _start at ./client.jl:550 jfptr__start_97682.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7fd5883fc249) 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) ┌ 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/v1.12/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007d968fdfc010 Total snapshots: 711. Utilization: 100% ╎708 @Base/client.jl:550 _start() ╎ 708 @Base/client.jl:283 exec_options(opts::Base.JLOptions) ╎ 708 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 708 @Base/Base.jl:308 (::Base.IncludeInto)(fname::String) ╎ 708 @Base/Base.jl:307 include(mapexpr::Function, mod::Module, _path::St… ╎ 708 @Base/loading.jl:2903 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 708 @Base/loading.jl:2843 include_string(mapexpr::typeof(identity), m… ╎ ╎ 708 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 708 @Base/Base.jl:308 (::Base.IncludeInto)(fname::String) ╎ ╎ 708 @Base/Base.jl:307 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 708 @Base/loading.jl:2903 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 708 @Base/loading.jl:2843 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 708 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 708 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 708 @Test/src/Test.jl:1776 macro expansion ╎ ╎ ╎ 708 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 708 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… 1╎ ╎ ╎ ╎ 98 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 16 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 16 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 9 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:920 getindex ╎ ╎ ╎ ╎ ╎ 2 @Base/…ators.jl:425 > 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 4 @VCFTools/…t.jl:225 geno_ismissing 1╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:919 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:11 length 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:920 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:132 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:920 getindex ╎ ╎ ╎ ╎ 3 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:3134 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:0 _getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:952 _getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:939 _in_unit_range 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:920 getindex 1╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:134 gtstats(record::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:920 getindex ╎ ╎ ╎ ╎ 66 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 65 @Base/array.jl:2441 findfirst ╎ ╎ ╎ ╎ 64 @Base/array.jl:2390 findnext 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:919 getindex 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:920 getindex ╎ ╎ ╎ ╎ ╎ 59 @Base/…ators.jl:1194 Fix ╎ ╎ ╎ ╎ ╎ 59 @Base/…tors.jl:1194 #_#58 ╎ ╎ ╎ ╎ ╎ 59 @Base/…tors.jl:178 isequal 59╎ ╎ ╎ ╎ ╎ 59 @Base/…ring.jl:163 == ╎ ╎ ╎ ╎ 1 @Base/array.jl:2391 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:920 getindex ╎ ╎ ╎ ╎ 8 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 8 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 8 @Base/array.jl:2441 findfirst ╎ ╎ ╎ ╎ ╎ 8 @Base/array.jl:2390 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:920 getindex ╎ ╎ ╎ ╎ ╎ 7 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:672 isequaldata ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:776 length 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ ╎ ╎ 6 @VariantCallFormat/…:673 isequaldata ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:1258 pointer ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1255 pointer 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…nter.jl:63 cconvert 5╎ ╎ ╎ ╎ ╎ 5 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:920 getindex ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:82 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:919 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:920 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:83 aim_select(record::VariantCallFo… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:920 getindex ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:85 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/bool.jl:168 + 1╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:920 getindex ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:99 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:261 log(x::Float64) ╎ ╎ ╎ ╎ 1 @Base/…al/log.jl:289 _log ╎ ╎ ╎ ╎ ╎ 1 @Base/…l/log.jl:163 log_proc1 1╎ ╎ ╎ ╎ ╎ 1 @Base/float.jl:495 + ╎ ╎ ╎ ╎ 610 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 610 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 110 @BioGenerics/…jl:87 iterate ╎ ╎ ╎ ╎ 110 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… 1╎ ╎ ╎ ╎ ╎ 110 @VariantCallFormat/…:142 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:156 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 1 @VariantCallFormat/…:78 initialize!(record::Vari… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:2066 empty! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1229 _deleteend! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:219 _unsetindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ 75 @VariantCallFormat/…:165 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 65 @Automa/…en.jl:449 macro expansion ╎ ╎ ╎ ╎ ╎ 18 @Base/array.jl:405 getindex 18╎ ╎ ╎ ╎ ╎ 18 @Base/boot.jl:648 Array ╎ ╎ ╎ ╎ ╎ 44 @Base/array.jl:1286 push! ╎ ╎ ╎ ╎ ╎ 41 @Base/…ray.jl:1289 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1122 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:54 getproperty 1╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:1130 _growend! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:83 < 6╎ ╎ ╎ ╎ ╎ ╎ 37 @Base/…ray.jl:1131 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ay.jl:1148 (::Base.var"#_growend!##0#… ╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ay.jl:1067 array_new_memory 21╎ ╎ ╎ ╎ ╎ ╎ 21 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1151 (::Base.var"#_growend!##0#… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:594 memoryref 9╎ ╎ ╎ ╎ ╎ ╎ 9 @Base/…ay.jl:1156 (::Base.var"#_growend!##0#… ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:1290 _push! 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ray.jl:1010 __safe_setindex! 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:919 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:920 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:455 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:565 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:262 & ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…sics.jl:235 and ╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:235 and 2╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:243 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:572 macro expansion ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…yops.jl:50 vload ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…sics.jl:470 load 3╎ ╎ ╎ ╎ ╎ ╎ 3 @SIMD/…ics.jl:479 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:575 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:481 all ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…dvec.jl:476 reduce ╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:832 reduce_and 2╎ ╎ ╎ ╎ ╎ ╎ 2 @SIMD/…ics.jl:847 macro expansion 2╎ ╎ ╎ ╎ ╎ 2 @Automa/…en.jl:584 macro expansion ╎ ╎ ╎ ╎ ╎ 33 @VariantCallFormat/…:181 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 33 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 33 @BufferedStreams/…:71 fillbuffer!(stream::Buffe… ╎ ╎ ╎ ╎ ╎ 33 @BufferedStreams/…:5 readbytes! 1╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/io.jl:1151 readbytes!(s::TranscodingStr… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:209 eof ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:213 eof ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:222 sloweof(stream::T… ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:610 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:624 fillbuffer(stre… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:685 callprocess(st… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @CodecZlib/…:195 process(codec::GzipDec… 3╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 22 @Base/io.jl:1152 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 19 @TranscodingStreams/…:306 read ╎ ╎ ╎ ╎ ╎ ╎ 19 @Base/io.jl:349 peek ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:298 peek ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:208 eof 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:54 getproperty 2╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:209 eof ╎ ╎ ╎ ╎ ╎ ╎ 16 @TranscodingStreams/…:302 peek 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:54 getproperty 7╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…ls.jl:919 getindex 8╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ls.jl:920 getindex ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:307 read ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:97 consumed! ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:98 #consumed!#1 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:58 setproperty! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:87 + ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/io.jl:1158 readbytes!(s::TranscodingStr… ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ray.jl:398 setindex! ╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:986 setindex! 5╎ ╎ ╎ ╎ ╎ ╎ 5 @Base/…ay.jl:991 _setindex! ╎ ╎ ╎ ╎ 500 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 500 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:354 copy 3╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:588 GenericMemory 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:356 copy ╎ ╎ ╎ ╎ ╎ 496 @Base/…pcopy.jl:29 deepcopy ╎ ╎ ╎ ╎ ╎ 496 @Base/…pcopy.jl:128 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 496 @Base/…copy.jl:137 deepcopy_internal(x::MemoryRe… 4╎ ╎ ╎ ╎ ╎ 496 @Base/…copy.jl:99 deepcopy_internal 2╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:0 _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 6 @Base/…copy.jl:106 _deepcopy_memory_t(x::Memor… 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:588 GenericMemory 76╎ ╎ ╎ ╎ ╎ 77 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 16╎ ╎ ╎ ╎ ╎ 16 @Base/…copy.jl:112 _deepcopy_memory_t(x::Memor… 12╎ ╎ ╎ ╎ ╎ 12 @Base/…copy.jl:113 _deepcopy_memory_t(x::Memor… 25╎ ╎ ╎ ╎ ╎ 325 @Base/…copy.jl:115 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:0 deepcopy_internal(x::MemoryRe… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:123 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…opy.jl:124 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ct.jl:182 in 26╎ ╎ ╎ ╎ ╎ ╎ 28 @Base/…ct.jl:92 get 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:54 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 46 @Base/…opy.jl:127 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:660 Array 5╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ot.jl:648 Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:593 memoryref 40╎ ╎ ╎ ╎ ╎ ╎ 40 @Base/…ict.jl:86 setindex! 3╎ ╎ ╎ ╎ ╎ ╎ 223 @Base/…opy.jl:128 deepcopy_internal(x::Vector… 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…opy.jl:0 deepcopy_internal(x::MemoryR… ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…opy.jl:133 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ct.jl:182 in 62╎ ╎ ╎ ╎ ╎ ╎ 63 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:54 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 153 @Base/…opy.jl:137 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…opy.jl:96 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ct.jl:182 in 27╎ ╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ct.jl:92 get 15╎ ╎ ╎ ╎ ╎ ╎ 126 @Base/…opy.jl:99 deepcopy_internal 7╎ ╎ ╎ ╎ ╎ ╎ 7 @Base/…py.jl:102 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:103 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:831 isbitstype 26╎ ╎ ╎ ╎ ╎ ╎ 103 @Base/…py.jl:104 _deepcopy_memory_t(x::Mem… 6╎ ╎ ╎ ╎ ╎ ╎ 6 @Base/…ry.jl:175 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:179 copy(a::Memory{UnitRange… 14╎ ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:180 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ry.jl:143 unsafe_copyto! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ry.jl:119 unsafe_copyto! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…ry.jl:125 unsafe_copyto! 12╎ ╎ ╎ ╎ ╎ ╎ ╎ 12 @Base/…em.jl:28 memmove 42╎ ╎ ╎ ╎ ╎ ╎ 43 @Base/…ct.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:58 setproperty! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…opy.jl:140 deepcopy_internal(x::Memor… 41╎ ╎ ╎ ╎ ╎ 41 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 13╎ ╎ ╎ ╎ ╎ 13 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… ============================================================== 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/v1.12/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007fd56e1fc010 Total snapshots: 408. Utilization: 0% ╎408 @Base/client.jl:550 _start() ╎ 408 @Base/client.jl:317 exec_options(opts::Base.JLOptions) ╎ 408 @Base/Base.jl:306 include(mod::Module, _path::String) ╎ 408 @Base/loading.jl:2903 _include(mapexpr::Function, mod::Module, _pat… ╎ 408 @Base/loading.jl:2843 include_string(mapexpr::typeof(identity), mo… ╎ 408 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 408 @Pkg/src/API.jl:151 kwcall(::@NamedTuple{julia_args::Cmd}, ::typ… ╎ ╎ 408 @Pkg/src/API.jl:151 #test#81 ╎ ╎ 408 @Pkg/src/API.jl:152 test ╎ ╎ 408 @Pkg/src/API.jl:152 test(pkgs::Vector{String}; kwargs::Base.P… ╎ ╎ 408 @Pkg/src/API.jl:153 kwcall(::@NamedTuple{julia_args::Cmd}, :… ╎ ╎ ╎ 408 @Pkg/src/API.jl:164 test(pkgs::Vector{PackageSpec}; io::IOC… ╎ ╎ ╎ 408 @Pkg/src/API.jl:462 kwcall(::@NamedTuple{julia_args::Cmd, … ╎ ╎ ╎ 408 @Pkg/src/API.jl:483 test(ctx::Pkg.Types.Context, pkgs::Ve… ╎ ╎ ╎ 408 @Pkg/…erations.jl:2280 test ╎ ╎ ╎ 408 @Pkg/…erations.jl:2370 test(ctx::Pkg.Types.Context, pkg… ╎ ╎ ╎ ╎ 408 @Pkg/…rations.jl:2110 kwcall(::@NamedTuple{preferences… ╎ ╎ ╎ ╎ 408 @Pkg/…rations.jl:2118 #sandbox#181 ╎ ╎ ╎ ╎ 408 @Base/file.jl:895 mktempdir(fn::Function) ╎ ╎ ╎ ╎ 408 @Base/file.jl:895 mktempdir(fn::Function, parent::S… ╎ ╎ ╎ ╎ 408 @Base/file.jl:899 mktempdir(fn::Pkg.Operations.var… ╎ ╎ ╎ ╎ ╎ 408 @Pkg/…tions.jl:2171 (::Pkg.Operations.var"#185#18… ╎ ╎ ╎ ╎ ╎ 408 @Pkg/…tions.jl:2062 with_temp_env(fn::Pkg.Operat… ╎ ╎ ╎ ╎ ╎ 408 @Pkg/…tions.jl:2204 (::Pkg.Operations.var"#189#… ╎ ╎ ╎ ╎ ╎ 408 @Base/env.jl:265 withenv(::Pkg.Operations.var"… ╎ ╎ ╎ ╎ ╎ 408 @Pkg/…ions.jl:2385 (::Pkg.Operations.var"#204… ╎ ╎ ╎ ╎ ╎ ╎ 408 @Pkg/…ons.jl:2445 subprocess_handler(cmd::Cm… ╎ ╎ ╎ ╎ ╎ ╎ 408 @Base/…ss.jl:687 wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 408 @Base/…ss.jl:694 wait(x::Base.Process, syn… ╎ ╎ ╎ ╎ ╎ ╎ 408 @Base/…on.jl:136 wait ╎ ╎ ╎ ╎ ╎ ╎ 408 @Base/…on.jl:141 wait(c::Base.GenericCon… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 408 @Base/…sk.jl:1199 wait() 407╎ ╎ ╎ ╎ ╎ ╎ ╎ 408 @Base/…sk.jl:1187 poptask(W::Base.Intr… [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 poptask at ./task.jl:1187 wait at ./task.jl:1199 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 profile_printing_listener at ./Base.jl:332 #start_profile_listener##0 at ./Base.jl:352 jfptr_YY.start_profile_listenerYY.YY.0_50938.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 25988900 (Pool: 25988244; Big: 656); GC: 24 [431] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 _setindex! at ./array.jl:991 [inlined] setindex! at ./array.jl:986 [inlined] setindex! at ./subarray.jl:398 [inlined] readbytes! at ./io.jl:1158 readbytes! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/io.jl:5 [inlined] fillbuffer! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/bufferedinputstream.jl:71 fillbuffer! at /home/pkgeval/.julia/packages/BufferedStreams/YvcPf/src/bufferedinputstream.jl:61 [inlined] _read! at /home/pkgeval/.julia/packages/VariantCallFormat/DDn3I/src/ReaderHelper.jl:181 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 read! at /home/pkgeval/.julia/packages/VariantCallFormat/DDn3I/src/ReaderHelper.jl:142 tryread! at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:76 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:87 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x7d967b42ac36) at (unknown file) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_invoke at /source/src/gf.c:4017 jl_toplevel_eval_flex at /source/src/toplevel.c:1024 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2903 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_91637.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2843 _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 _include at ./loading.jl:2903 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_91637.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:693 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 exec_options at ./client.jl:283 _start at ./client.jl:550 jfptr__start_97682.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4010 [inlined] ijl_apply_generic at /source/src/gf.c:4210 jl_apply at /source/src/julia.h:2387 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7d96aa0c3249) 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: 18025764329 (Pool: 18025748820; Big: 15509); GC: 30187 PkgEval terminated after 2726.4s: test duration exceeded the time limit