Package evaluation of VCFTools on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T14:49:12.226 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 12.37s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath ─────────────────── v0.8.0 Installed IrrationalConstants ───── v0.2.4 Installed PtrArrays ─────────────── v1.3.0 Installed BioGenerics ───────────── v0.1.5 Installed StatsFuns ─────────────── v1.4.0 Installed HypergeometricFunctions ─ v0.3.28 Installed Accessors ─────────────── v0.1.42 Installed Preferences ───────────── v1.4.3 Installed DataAPI ───────────────── v1.16.0 Installed PDMats ────────────────── v0.11.33 Installed JLLWrappers ───────────── v1.7.0 Installed BGZFStreams ───────────── v0.3.2 Installed ProgressMeter ─────────── v1.10.4 Installed ConstructionBase ──────── v1.5.8 Installed Roots ─────────────────── v2.2.7 Installed SpecialFunctions ──────── v2.5.0 Installed DelimitedFiles ────────── v1.9.1 Installed OrderedCollections ────── v1.8.0 Installed QuadGK ────────────────── v2.11.2 Installed TranscodingStreams ────── v0.9.13 Installed FillArrays ────────────── v1.13.0 Installed HypothesisTests ───────── v0.11.5 Installed Rmath_jll ─────────────── v0.5.1+0 Installed Reexport ──────────────── v1.2.2 Installed LogExpFunctions ───────── v0.3.29 Installed Statistics ────────────── v1.11.1 Installed DataStructures ────────── v0.18.22 Installed VariantCallFormat ─────── v0.5.6 Installed Combinatorics ─────────── v1.0.2 Installed VCFTools ──────────────── v0.2.10 Installed BufferedStreams ───────── v1.2.2 Installed StatsAPI ──────────────── v1.7.0 Installed Compat ────────────────── v4.16.0 Installed CompositionsBase ──────── v0.1.2 Installed AliasTables ───────────── v1.1.3 Installed MacroTools ────────────── v0.5.15 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Automa ────────────────── v0.8.4 Installed Distributions ─────────── v0.25.118 Installed CodecZlib ─────────────── v0.7.8 Installed Missings ──────────────── v1.2.0 Installed InverseFunctions ──────── v0.1.17 Installed CommonSolve ───────────── v0.2.4 Installed DocStringExtensions ───── v0.9.4 Installed StatsBase ─────────────── v0.34.4 Installed SortingAlgorithms ─────── v1.2.1 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 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 v1.0.2 [38540f10] + CommonSolve v0.2.4 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [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 v0.5.15 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 [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 v2.2.7 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.4.0 ⌅ [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 [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 [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 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [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 6.47s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 3333.4 ms ✓ TestEnv 1 dependency successfully precompiled in 3 seconds. 23 already precompiled. Precompiling package dependencies... Precompilation completed after 397.53s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_qG4JD7/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.118 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.10.4 [276daf66] SpecialFunctions v2.5.0 [2913bbd2] StatsBase v0.34.4 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [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_qG4JD7/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 v1.0.2 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.16.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.5.8 [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 v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.3 [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 v0.5.15 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [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 v2.2.7 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.4.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 ⌅ [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 v1.6.0 [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 [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 [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... Test Summary: | Pass Total Time H-W test | 1 1 2.7s Test Summary: | Pass Total Time openvcf | 4 4 2.0s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 3.0s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.5s ┌ 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: 0:35:45 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 13.970521 seconds (7.38 M allocations: 450.533 MiB, 3.96% gc time, 92.20% compilation time) 0.730545 seconds (2.85 M allocations: 195.074 MiB, 5.40% gc time, 13.29% compilation time) Progress: 0%| | ETA: 0:32:19 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.563663 seconds (4.29 M allocations: 292.203 MiB, 2.07% gc time, 80.35% compilation time) 0.674670 seconds (2.85 M allocations: 195.311 MiB, 4.19% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.8s 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 2.5s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.4s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.2s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 2.8s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:25:06 Progress: 0%| | ETA: 0:23:52 Progress: 0%|▏ | ETA: 0:23:31 Progress: 0%|▏ | ETA: 0:23:18 Progress: 0%|▏ | ETA: 0:22:34 Progress: 0%|▏ | ETA: 0:22:17 Progress: 1%|▎ | ETA: 0:22:19 Progress: 1%|▎ | ETA: 0:22:21 Progress: 1%|▎ | ETA: 0:22:23 Progress: 1%|▎ | ETA: 0:22:24 Progress: 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Progress: 100%|█████████████████████████████████████████| Time: 0:02:18 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 23:19:57 Progress: 18%|███████▌ | ETA: 0:09:16 Progress: 38%|███████████████▍ | ETA: 0:03:30 Progress: 58%|███████████████████████▉ | ETA: 0:01:31 Progress: 79%|████████████████████████████████▍ | ETA: 0:00:34 Progress: 99%|████████████████████████████████████████▌| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:02:09 [ Info: 823 records are matched 285.970251 seconds (2.19 G allocations: 143.698 GiB, 5.44% gc time, 0.05% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:24:06 Progress: 0%| | ETA: 0:22:54 Progress: 0%|▏ | ETA: 0:22:20 Progress: 0%|▏ | ETA: 0:22:21 Progress: 0%|▏ | ETA: 0:22:13 Progress: 0%|▏ | ETA: 0:22:15 Progress: 1%|▎ | ETA: 0:21:59 Progress: 1%|▎ | ETA: 0:21:55 Progress: 1%|▎ | ETA: 0:21:43 Progress: 1%|▍ | ETA: 0:21:39 Progress: 1%|▍ | ETA: 0:21:35 Progress: 1%|▍ | ETA: 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0%| | ETA: 23:06:25 Progress: 15%|██████▎ | ETA: 0:11:32 Progress: 33%|█████████████▋ | ETA: 0:04:11 Progress: 51%|████████████████████▉ | ETA: 0:02:02 Progress: 68%|████████████████████████████ | ETA: 0:00:59 Progress: 87%|███████████████████████████████████▋ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:02:08 [ Info: 488 records are matched 281.490596 seconds (2.19 G allocations: 143.692 GiB, 5.52% gc time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:09 Progress: 0%|▏ | ETA: 0:20:02 Progress: 0%|▏ | ETA: 0:19:50 Progress: 0%|▏ | ETA: 0:19:45 Progress: 0%|▏ | ETA: 0:19:40 Progress: 1%|▎ | ETA: 0:19:37 Progress: 1%|▎ | ETA: 0:19:36 Progress: 1%|▎ | ETA: 0:19:30 Progress: 1%|▍ | ETA: 0:19:24 Progress: 1%|▍ | ETA: 0:19:19 Progress: 1%|▍ | ETA: 0:19:18 Progress: 1%|▍ | ETA: 0:19:19 Progress: 1%|▌ | ETA: 0:19:20 Progress: 1%|▌ | ETA: 0:19:20 Progress: 1%|▌ | ETA: 0:19:20 Progress: 1%|▌ | ETA: 0:19:20 Progress: 1%|▋ | ETA: 0:19:21 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10%|███▉ | ETA: 0:17:46 Progress: 10%|████ | ETA: 0:17:45 Progress: 10%|████ | ETA: 0:17:44 Progress: 10%|████ | ETA: 0:17:42 Progress: 10%|████▏ | ETA: 0:17:41 Progress: 10%|████▏ | ETA: 0:17:40 Progress: 10%|████▏ | ETA: 0:17:39 Progress: 10%|████▏ | ETA: 0:17:38 Progress: 10%|████▎ | ETA: 0:17:37 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 1 days, 0:37:19 Progress: 15%|██████▎ | ETA: 0:12:12 Progress: 33%|█████████████▍ | ETA: 0:04:36 Progress: 50%|████████████████████▌ | ETA: 0:02:15 Progress: 67%|███████████████████████████▌ | ETA: 0:01:06 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:26 Progress: 100%|█████████████████████████████████████████| Time: 0:02:16 [ Info: 0 records are matched 276.135710 seconds (2.19 G allocations: 143.692 GiB, 5.25% gc time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 14m11.1s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 1:08:22 Progress: 15%|██████▏ | ETA: 0:12:54 Progress: 31%|████████████▋ | ETA: 0:05:03 Progress: 47%|███████████████████▎ | ETA: 0:02:34 Progress: 63%|██████████████████████████ | ETA: 0:01:20 Progress: 81%|█████████████████████████████████▍ | ETA: 0:00:32 Progress: 99%|████████████████████████████████████████▉| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:02:19 [ Info: 833 records are matched 156.428087 seconds (1.11 G allocations: 72.784 GiB, 5.15% gc time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 0:15:16 Progress: 16%|██████▍ | ETA: 0:11:45 Progress: 33%|█████████████▍ | ETA: 0:04:31 Progress: 50%|████████████████████▌ | ETA: 0:02:12 Progress: 68%|███████████████████████████▊ | ETA: 0:01:04 Progress: 86%|███████████████████████████████████▎ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:02:14 [ Info: 493 records are matched 151.629021 seconds (1.11 G allocations: 72.784 GiB, 5.12% gc time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 0:01:42 Progress: 17%|██████▉ | ETA: 0:10:40 Progress: 34%|██████████████ | ETA: 0:04:09 Progress: 53%|█████████████████████▊ | ETA: 0:01:56 Progress: 71%|█████████████████████████████▎ | ETA: 0:00:53 Progress: 91%|█████████████████████████████████████▍ | ETA: 0:00:13 Progress: 100%|█████████████████████████████████████████| Time: 0:02:13 [ Info: 0 records are matched 150.192666 seconds (1.11 G allocations: 72.784 GiB, 5.13% gc time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 7m41.0s 1.960888 seconds (1.38 M allocations: 92.636 MiB, 1.74% gc time, 91.10% compilation time) 1.472057 seconds (1.16 M allocations: 83.387 MiB, 1.97% gc time, 85.64% compilation time) 1.433637 seconds (1.17 M allocations: 82.671 MiB, 1.41% gc time, 88.45% compilation time) 1.114975 seconds (312.96 k allocations: 16.035 MiB, 99.98% compilation time) 0.015607 seconds (10.10 k allocations: 672.547 KiB, 97.02% compilation time) 0.012663 seconds (2.63 k allocations: 242.789 KiB, 96.13% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 13.6s 0.583223 seconds (605.63 k allocations: 54.885 MiB, 4.70% gc time, 70.45% compilation time) 0.160280 seconds (523.79 k allocations: 52.393 MiB, 11.16% gc time, 9.29% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 2.9s Test Summary: | Pass Total Time convert_ds | 5 5 1.4s 0.173477 seconds (524.94 k allocations: 50.413 MiB, 23.21% gc time, 24.01% compilation time) 0.120258 seconds (520.50 k allocations: 50.187 MiB, 11.96% gc time, 10.71% 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 0.096421 seconds (520.44 k allocations: 51.912 MiB) 0.136044 seconds (520.48 k allocations: 51.915 MiB, 13.46% gc time, 10.71% 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 0.149304 seconds (2.07 M allocations: 95.631 MiB, 5.07% gc time) 0.171702 seconds (2.07 M allocations: 95.635 MiB, 8.07% gc time, 8.21% 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 1.9s Test Summary: | Pass Total Time record info | 14 14 10.8s Test Summary: | Pass Total Time write VCF | 3 3 5.7s 1.271878 seconds (4.89 M allocations: 358.746 MiB, 6.50% gc time) 1.040749 seconds (2.83 M allocations: 193.181 MiB, 4.16% gc time) 1.651911 seconds (4.89 M allocations: 358.312 MiB, 23.45% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.3s 1.311358 seconds (613.78 k allocations: 53.429 MiB, 44.62% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 4.9s Test Summary: | Pass Total Time filter_chr | 4 4 1.8s Progress: 0%|▏ | ETA: 0:22:48 Progress: 1%|▎ | ETA: 0:22:23 Progress: 1%|▌ | ETA: 0:22:27 Progress: 1%|▋ | ETA: 0:23:10 Progress: 2%|▊ | ETA: 0:23:27 Progress: 2%|▉ | ETA: 0:23:43 Progress: 2%|█ | ETA: 0:23:57 Progress: 3%|█▏ | ETA: 0:24:07 Progress: 3%|█▎ | ETA: 0:24:28 Progress: 3%|█▍ | ETA: 0:24:29 Progress: 4%|█▌ | ETA: 0:24:23 Progress: 4%|█▋ | ETA: 0:24:22 Progress: 4%|█▊ | ETA: 0:24:21 Progress: 5%|█▉ | ETA: 0:24:21 Progress: 5%|██ | ETA: 0:24:19 Progress: 5%|██▏ | ETA: 0:24:20 Progress: 6%|██▎ | ETA: 0:24:19 Progress: 6%|██▍ | ETA: 0:24:16 Progress: 6%|██▋ | ETA: 0:24:14 Progress: 7%|██▊ | ETA: 0:24:10 Progress: 7%|██▉ | ETA: 0:24:07 Progress: 7%|███ | ETA: 0:24:04 Progress: 8%|███▏ | ETA: 0:24:01 Progress: 8%|███▎ | ETA: 0:23:58 Progress: 8%|███▍ | ETA: 0:23:55 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received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 417 running 1 of 1 signal (10): User defined signal 1 jl_lookup_generic_ at /source/src/gf.c:3047 [inlined] ijl_apply_generic at /source/src/gf.c:3121 _deepcopy_memory_t at ./deepcopy.jl:104 deepcopy_internal at ./deepcopy.jl:99 [inlined] deepcopy_internal at ./deepcopy.jl:137 deepcopy_internal at ./deepcopy.jl:128 unknown function (ip: 0x7b2178b33a86) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _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/YgfJC/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:1704 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_invoke at /source/src/gf.c:2955 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:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _include at ./loading.jl:2794 include at ./sysimg.jl:38 unknown function (ip: 0x7b2178a94082) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _include at ./loading.jl:2794 include at ./sysimg.jl:38 unknown function (ip: 0x7b2178a94082) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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:296 _start at ./client.jl:531 jfptr__start_73523.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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: 0x7b2179d66249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) Progress: 49%|████████████████████▏ | ETA: 0:12:30 ============================================================== Profile collected. A report will print at the next yield point ============================================================== Progress: 50%|████████████████████▎ | ETA: 0:12:24┌ 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 0x00007b216c800010 Total snapshots: 364. Utilization: 100% ╎364 @Base/client.jl:531; _start() ╎ 364 @Base/client.jl:296; exec_options(opts::Base.JLOptions) ╎ 364 @Base/boot.jl:430; eval ╎ 364 @Base/sysimg.jl:38; include(fname::String) ╎ 364 @Base/loading.jl:2794; _include(mapexpr::Function, mod::Module, _pat… ╎ 364 @Base/loading.jl:2734; include_string(mapexpr::typeof(identity), mo… ╎ ╎ 364 @Base/boot.jl:430; eval ╎ ╎ 364 @Base/sysimg.jl:38; include(fname::String) ╎ ╎ 364 @Base/loading.jl:2794; _include(mapexpr::Function, mod::Module, … ╎ ╎ 364 @Base/loading.jl:2734; include_string(mapexpr::typeof(identity)… ╎ ╎ 364 @Base/boot.jl:430; eval ╎ ╎ ╎ 364 …ls/test/aim_test.jl:3; top-level scope ╎ ╎ ╎ 364 @Test/src/Test.jl:1704; macro expansion ╎ ╎ ╎ 364 …s/test/aim_test.jl:19; macro expansion ╎ ╎ ╎ 364 …src/aim_select.jl:26; aim_select 2╎ ╎ ╎ 42 …src/aim_select.jl:44; aim_select(vcffile::String, sample… ╎ ╎ ╎ ╎ 11 …src/aim_select.jl:65; aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 11 …s/src/gtstats.jl:122; gtstats ╎ ╎ ╎ ╎ 8 …/src/gtstats.jl:127; gtstats(record::VariantCallForma… ╎ ╎ ╎ ╎ 2 …bstractarray.jl:426; lastindex ╎ ╎ ╎ ╎ 2 …bstractarray.jl:389; eachindex ╎ ╎ ╎ ╎ ╎ 2 …stractarray.jl:137; axes1 ╎ ╎ ╎ ╎ ╎ 2 …stractarray.jl:98; axes 2╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:194; size 4╎ ╎ ╎ ╎ 4 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 2 …/src/convert.jl:225; geno_ismissing 2╎ ╎ ╎ ╎ 2 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 1 …/src/gtstats.jl:132; gtstats(record::VariantCallForma… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3077; getindex 1╎ ╎ ╎ ╎ 1 @Base/range.jl:939; _getindex ╎ ╎ ╎ ╎ 2 …/src/gtstats.jl:133; gtstats(record::VariantCallForma… ╎ ╎ ╎ ╎ 1 @Base/array.jl:3077; getindex 1╎ ╎ ╎ ╎ 1 @Base/range.jl:939; _getindex 1╎ ╎ ╎ ╎ 1 @Base/int.jl:87; + ╎ ╎ ╎ ╎ 28 …src/aim_select.jl:74; aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 28 @Base/array.jl:2404; findfirst ╎ ╎ ╎ ╎ 28 @Base/array.jl:2353; findnext 6╎ ╎ ╎ ╎ 6 …e/essentials.jl:917; getindex ╎ ╎ ╎ ╎ 22 …se/operators.jl:1144; Fix2 ╎ ╎ ╎ ╎ 22 …se/operators.jl:134; isequal 22╎ ╎ ╎ ╎ ╎ 22 …ings/string.jl:162; == ╎ ╎ ╎ ╎ 1 …src/aim_select.jl:79; aim_select(record::VariantCallFor… ╎ ╎ ╎ ╎ 1 …s/src/convert.jl:225; geno_ismissing 1╎ ╎ ╎ ╎ 1 …e/essentials.jl:916; getindex ╎ ╎ ╎ 322 …src/aim_select.jl:46; aim_select(vcffile::String, sample… ╎ ╎ ╎ ╎ 322 …ase/iterators.jl:206; iterate ╎ ╎ ╎ ╎ 47 …nerics/src/IO.jl:87; iterate 1╎ ╎ ╎ ╎ 1 …nerics/src/IO.jl:75; tryread!(reader::VariantCallForm… ╎ ╎ ╎ ╎ 46 …nerics/src/IO.jl:76; tryread!(reader::VariantCallForm… ╎ ╎ ╎ ╎ 46 …ReaderHelper.jl:147; read!(reader::VariantCallFormat… ╎ ╎ ╎ ╎ 2 …ReaderHelper.jl:160; _read!(reader::VariantCallForm… ╎ ╎ ╎ ╎ ╎ 2 …t/src/record.jl:78; initialize!(record::VariantCal… ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:2029; empty! ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:1207; _deleteend! ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:218; _unsetindex! 1╎ ╎ ╎ ╎ ╎ 1 …tractarray.jl:699; checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:219; _unsetindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:524; memoryref ╎ ╎ ╎ ╎ 42 …ReaderHelper.jl:169; _read!(reader::VariantCallForm… ╎ ╎ ╎ ╎ ╎ 37 …src/codegen.jl:263; macro expansion ╎ ╎ ╎ ╎ ╎ 8 @Base/array.jl:400; getindex 7╎ ╎ ╎ ╎ ╎ 8 @Base/boot.jl:579; Array 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:522; memoryref(mem::Memory{UnitRan… ╎ ╎ ╎ ╎ ╎ 25 @Base/array.jl:1261; push! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1115; _growend! 1╎ ╎ ╎ ╎ ╎ 24 @Base/array.jl:1116; _growend! 4╎ ╎ ╎ ╎ ╎ 4 @Base/array.jl:1116; (::Base.var"#133#134"{Vecto… ╎ ╎ ╎ ╎ ╎ 9 @Base/array.jl:1129; (::Base.var"#133#134"{Vecto… ╎ ╎ ╎ ╎ ╎ 9 …ase/array.jl:1058; array_new_memory 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:512; GenericMemory 8╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/boot.jl:516; GenericMemory ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:1132; (::Base.var"#133#134"{Vecto… 3╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:523; memoryref 7╎ ╎ ╎ ╎ ╎ 7 @Base/array.jl:1134; (::Base.var"#133#134"{Vecto… ╎ ╎ ╎ ╎ ╎ 4 @Base/array.jl:1262; push! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0; __safe_setindex! 2╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:1001; __safe_setindex! 1╎ ╎ ╎ ╎ ╎ 1 …essentials.jl:11; length ╎ ╎ ╎ ╎ ╎ 3 …src/codegen.jl:291; macro expansion ╎ ╎ ╎ ╎ ╎ 3 …/src/memory.jl:56; getindex 2╎ ╎ ╎ ╎ ╎ 3 …/src/memory.jl:49; checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:520; <= 1╎ ╎ ╎ ╎ ╎ 2 …src/codegen.jl:292; macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1426; in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:38; & ╎ ╎ ╎ ╎ 2 …ReaderHelper.jl:185; _read!(reader::VariantCallForm… ╎ ╎ ╎ ╎ ╎ 2 …dinputstream.jl:61; fillbuffer! ╎ ╎ ╎ ╎ ╎ 2 …inputstream.jl:71; fillbuffer! ╎ ╎ ╎ ╎ ╎ 2 …eams/src/io.jl:5; readbytes! ╎ ╎ ╎ ╎ ╎ 2 …src/stream.jl:387; readbytes!(stream::Transcodi… ╎ ╎ ╎ ╎ ╎ 2 …src/stream.jl:201; eof(stream::TranscodingStre… ╎ ╎ ╎ ╎ ╎ ╎ 2 …rc/stream.jl:582; fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 2 …rc/stream.jl:596; fillbuffer(stream::Transco… ╎ ╎ ╎ ╎ ╎ ╎ 2 …c/stream.jl:656; callprocess(stream::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 2 …pression.jl:195; process(codec::GzipDecomp… 2╎ ╎ ╎ ╎ ╎ ╎ 2 …src/libz.jl:127; inflate! ╎ ╎ ╎ ╎ 275 …nerics/src/IO.jl:90; iterate ╎ ╎ ╎ ╎ 275 …t/src/record.jl:309; copy(record::VariantCallFormat.R… 1╎ ╎ ╎ ╎ 1 @Base/array.jl:350; copy ╎ ╎ ╎ ╎ 274 …ase/deepcopy.jl:29; deepcopy ╎ ╎ ╎ ╎ 274 …ase/deepcopy.jl:128; deepcopy_internal(x::Vector{Ve… ╎ ╎ ╎ ╎ ╎ 1 …se/deepcopy.jl:133; deepcopy_internal(x::MemoryRef… ╎ ╎ ╎ ╎ ╎ 1 …bstractdict.jl:19; haskey ╎ ╎ ╎ ╎ ╎ 1 …ase/iddict.jl:182; in 1╎ ╎ ╎ ╎ ╎ 1 …ase/iddict.jl:92; get ╎ ╎ ╎ ╎ ╎ 273 …se/deepcopy.jl:137; deepcopy_internal(x::MemoryRef… 2╎ ╎ ╎ ╎ ╎ 273 …se/deepcopy.jl:99; deepcopy_internal 35╎ ╎ ╎ ╎ ╎ 35 …e/deepcopy.jl:111; _deepcopy_memory_t(x::Memory,… 7╎ ╎ ╎ ╎ ╎ 7 …e/deepcopy.jl:112; _deepcopy_memory_t(x::Memory,… 35╎ ╎ ╎ ╎ ╎ 35 …e/deepcopy.jl:113; _deepcopy_memory_t(x::Memory,… 2╎ ╎ ╎ ╎ ╎ 2 …e/deepcopy.jl:114; _deepcopy_memory_t(x::Memory,… 6╎ ╎ ╎ ╎ ╎ 165 …e/deepcopy.jl:115; _deepcopy_memory_t(x::Memory,… 1╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:123; deepcopy_internal(x::Vector{… ╎ ╎ ╎ ╎ ╎ 10 …e/deepcopy.jl:124; deepcopy_internal(x::Vector{… ╎ ╎ ╎ ╎ ╎ 10 …stractdict.jl:19; haskey ╎ ╎ ╎ ╎ ╎ ╎ 10 …se/iddict.jl:182; in 10╎ ╎ ╎ ╎ ╎ ╎ 10 …se/iddict.jl:92; get ╎ ╎ ╎ ╎ ╎ 31 …e/deepcopy.jl:127; deepcopy_internal(x::Vector{… ╎ ╎ ╎ ╎ ╎ 5 @Base/boot.jl:591; Array ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:578; Array 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:514; GenericMemory 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:579; Array 26╎ ╎ ╎ ╎ ╎ 26 …ase/iddict.jl:86; setindex! 1╎ ╎ ╎ ╎ ╎ 117 …e/deepcopy.jl:128; deepcopy_internal(x::Vector{… 3╎ ╎ ╎ ╎ ╎ 3 …e/deepcopy.jl:0; deepcopy_internal(x::MemoryRe… 1╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:132; deepcopy_internal(x::Memory… ╎ ╎ ╎ ╎ ╎ 36 …e/deepcopy.jl:133; deepcopy_internal(x::Memory… ╎ ╎ ╎ ╎ ╎ ╎ 36 …stractdict.jl:19; haskey ╎ ╎ ╎ ╎ ╎ ╎ 36 …se/iddict.jl:182; in 34╎ ╎ ╎ ╎ ╎ ╎ 36 …se/iddict.jl:92; get 2╎ ╎ ╎ ╎ ╎ ╎ 2 …ase/Base.jl:49; getproperty ╎ ╎ ╎ ╎ ╎ 73 …e/deepcopy.jl:137; deepcopy_internal(x::Memory… ╎ ╎ ╎ ╎ ╎ ╎ 11 …e/deepcopy.jl:96; deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 11 …tractdict.jl:19; haskey ╎ ╎ ╎ ╎ ╎ ╎ 11 …e/iddict.jl:182; in 9╎ ╎ ╎ ╎ ╎ ╎ 10 …e/iddict.jl:92; get 1╎ ╎ ╎ ╎ ╎ ╎ 1 …e/iddict.jl:93; get ╎ ╎ ╎ ╎ ╎ ╎ 62 …e/deepcopy.jl:99; deepcopy_internal 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/Base.jl:0; _deepcopy_memory_t(x::Memory… 4╎ ╎ ╎ ╎ ╎ ╎ 4 …/deepcopy.jl:102; _deepcopy_memory_t(x::Memo… 8╎ ╎ ╎ ╎ ╎ ╎ 57 …/deepcopy.jl:104; _deepcopy_memory_t(x::Memo… 22╎ ╎ ╎ ╎ ╎ ╎ 22 …icmemory.jl:170; copy(a::Memory{UnitRange{I… 26╎ ╎ ╎ ╎ ╎ ╎ 27 …e/iddict.jl:86; setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 …ase/Base.jl:53; setproperty! 2╎ ╎ ╎ ╎ ╎ 2 …e/deepcopy.jl:138; deepcopy_internal(x::Memory… ╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:139; deepcopy_internal(x::Memory… 1╎ ╎ ╎ ╎ ╎ ╎ 1 …promotion.jl:639; == 19╎ ╎ ╎ ╎ ╎ 19 …e/deepcopy.jl:117; _deepcopy_memory_t(x::Memory,… 7╎ ╎ ╎ ╎ ╎ 7 …e/deepcopy.jl:118; _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 1 …e/deepcopy.jl:120; _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:908; iterate 1╎ ╎ ╎ ╎ ╎ 1 …/promotion.jl:639; == ====================================================================================== 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#731 at ./condition.jl:130 wait at ./condition.jl:125 [inlined] wait at ./process.jl:694 wait at ./process.jl:687 unknown function (ip: 0x764758f72ea2) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 subprocess_handler at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2142 #131 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2082 withenv at ./env.jl:265 #118 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1931 with_temp_env at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1789 #116 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1898 #mktempdir#28 at ./file.jl:819 unknown function (ip: 0x764758f6b63d) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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:1845 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1837 unknown function (ip: 0x764758f5fc0a) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 #test#128 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2063 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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: 0x764758f5f90d) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 #test#77 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 unknown function (ip: 0x764758f5f2fd) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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: 0x764758f5b7a6) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _include at ./loading.jl:2794 include at ./Base.jl:557 jfptr_include_46977.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 exec_options at ./client.jl:323 _start at ./client.jl:531 jfptr__start_73523.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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: 0x76475a210249) __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: 50%|████████████████████▌ | ETA: 0:12:22┌ 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 0x000076474cc00010 Total snapshots: 21. Utilization: 0% ╎21 @Base/client.jl:531; _start() ╎ 21 @Base/client.jl:323; exec_options(opts::Base.JLOptions) ╎ 21 @Base/Base.jl:557; include(mod::Module, _path::String) ╎ 21 @Base/loading.jl:2794; _include(mapexpr::Function, mod::Module, _path:… ╎ 21 @Base/loading.jl:2734; include_string(mapexpr::typeof(identity), mod:… ╎ 21 @Base/boot.jl:430; eval ╎ ╎ 21 @Pkg/src/API.jl:146; kwcall(::@NamedTuple{julia_args::Cmd}, ::typeo… ╎ ╎ 21 @Pkg/src/API.jl:146; #test#74 ╎ ╎ 21 @Pkg/src/API.jl:147; test ╎ ╎ 21 @Pkg/src/API.jl:147; #test#75 ╎ ╎ 21 @Pkg/src/API.jl:148; kwcall(::@NamedTuple{julia_args::Cmd}, ::t… ╎ ╎ ╎ 21 @Pkg/src/API.jl:159; test(pkgs::Vector{Pkg.Types.PackageSpec};… ╎ ╎ ╎ 21 @Pkg/src/API.jl:460; kwcall(::@NamedTuple{julia_args::Cmd, io… ╎ ╎ ╎ 21 @Pkg/src/API.jl:481; test(ctx::Pkg.Types.Context, pkgs::Vect… ╎ ╎ ╎ 21 …src/Operations.jl:2007; test ╎ ╎ ╎ 21 …src/Operations.jl:2063; test(ctx::Pkg.Types.Context, pkgs… ╎ ╎ ╎ ╎ 21 …rc/Operations.jl:1837; kwcall(::@NamedTuple{preferences:… ╎ ╎ ╎ ╎ 21 …rc/Operations.jl:1845; #sandbox#115 ╎ ╎ ╎ ╎ 21 @Base/file.jl:815; mktempdir ╎ ╎ ╎ ╎ 21 @Base/file.jl:815; mktempdir(fn::Function, parent::Str… ╎ ╎ ╎ ╎ 21 @Base/file.jl:819; mktempdir(fn::Pkg.Operations.var"#… ╎ ╎ ╎ ╎ ╎ 21 …/Operations.jl:1898; (::Pkg.Operations.var"#116#121… ╎ ╎ ╎ ╎ ╎ 21 …/Operations.jl:1789; with_temp_env(fn::Pkg.Operati… ╎ ╎ ╎ ╎ ╎ 21 …Operations.jl:1931; (::Pkg.Operations.var"#118#12… ╎ ╎ ╎ ╎ ╎ 21 @Base/env.jl:265; withenv(::Pkg.Operations.var"#1… ╎ ╎ ╎ ╎ ╎ 21 …Operations.jl:2082; (::Pkg.Operations.var"#131#… ╎ ╎ ╎ ╎ ╎ ╎ 21 …perations.jl:2142; subprocess_handler(cmd::Cmd… ╎ ╎ ╎ ╎ ╎ ╎ 21 …e/process.jl:687; wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 21 …e/process.jl:694; wait(x::Base.Process, sync… ╎ ╎ ╎ ╎ ╎ ╎ 21 …ondition.jl:125; wait ╎ ╎ ╎ ╎ ╎ ╎ 21 …ondition.jl:130; wait(c::Base.GenericCondi… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 21 …ase/task.jl:1021; wait() 20╎ ╎ ╎ ╎ ╎ ╎ ╎ 21 …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) [417] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 gc_add_page at /source/src/gc.c:1303 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 jl_gc_pool_alloc_inner at /source/src/gc.c:1357 jl_gc_pool_alloc_noinline at /source/src/gc.c:1386 [inlined] jl_gc_alloc_ at /source/src/julia_internal.h:523 [inlined] jl_gc_alloc at /source/src/gc.c:3946 _new_genericmemory_ at /source/src/genericmemory.c:56 jl_genericmemory_copy_slice at /source/src/genericmemory.c:349 copy at ./genericmemory.jl:170 unknown function (ip: 0x7b2178b33ad2) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _deepcopy_memory_t at ./deepcopy.jl:104 deepcopy_internal at ./deepcopy.jl:99 [inlined] deepcopy_internal at ./deepcopy.jl:137 deepcopy_internal at ./deepcopy.jl:128 unknown function (ip: 0x7b2178b33a86) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _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/YgfJC/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:1704 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_invoke at /source/src/gf.c:2955 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:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 wait at ./task.jl:1021 _include at ./loading.jl:2794 include at ./sysimg.jl:38 unknown function (ip: 0x7b2178a94082) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] #wait#731 at ./condition.jl:130 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 wait at ./condition.jl:125 [inlined] _trywait at ./asyncevent.jl:145 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 profile_printing_listener at ./Base.jl:577 _include at ./loading.jl:2794 include at ./sysimg.jl:38 unknown function (ip: 0x7b2178a94082) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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 #1190 at ./Base.jl:617 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 jfptr_YY.1190_76096.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] start_task at /source/src/task.c:1202 unknown function (ip: (nil)) Allocations: 19825488 (Pool: 19824634; Big: 854); GC: 24 eval at ./boot.jl:430 [inlined] exec_options at ./client.jl:296 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") _start at ./client.jl:531 error at ./error.jl:35 jfptr__start_73523.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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: 0x7b2179d66249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) Allocations: 15312558375 (Pool: 15312542407; Big: 15968); GC: 27433 #schedule#761 at ./task.jl:884 schedule at ./task.jl:876 [inlined] uv_writecb_task at ./stream.jl:1200 jfptr_uv_writecb_task_67080.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jlcapi_uv_writecb_task_67543.1 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_48429.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 showerror at ./errorshow.jl:152 unknown function (ip: 0x764758f7f4b6) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _atexit at ./initdefs.jl:462 jfptr__atexit_69596.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 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 2722.33s: test duration exceeded the time limit