Package evaluation of VCFTools on Julia 1.13.0-DEV.888 (0e1aa6c7eb*) started at 2025-07-24T18:47:31.609 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 11.14s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CommonSolve ───────────── v0.2.4 Installed CompositionsBase ──────── v0.1.2 Installed DelimitedFiles ────────── v1.9.1 Installed MacroTools ────────────── v0.5.16 Installed FillArrays ────────────── v1.13.0 Installed DataStructures ────────── v0.18.22 Installed VCFTools ──────────────── v0.2.10 Installed HypergeometricFunctions ─ v0.3.28 Installed CodecZlib ─────────────── v0.7.8 Installed AliasTables ───────────── v1.1.3 Installed ConstructionBase ──────── v1.6.0 Installed OrderedCollections ────── v1.8.1 Installed StatsBase ─────────────── v0.34.5 Installed TranscodingStreams ────── v0.9.13 Installed Compat ────────────────── v4.17.0 Installed Combinatorics ─────────── v1.0.3 Installed DataAPI ───────────────── v1.16.0 Installed ProgressMeter ─────────── v1.10.4 Installed StatsAPI ──────────────── v1.7.1 Installed IrrationalConstants ───── v0.2.4 Installed Statistics ────────────── v1.11.1 Installed HypothesisTests ───────── v0.11.5 Installed QuadGK ────────────────── v2.11.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed LogExpFunctions ───────── v0.3.29 Installed Rmath ─────────────────── v0.8.0 Installed StatsFuns ─────────────── v1.5.0 Installed BufferedStreams ───────── v1.2.2 Installed PtrArrays ─────────────── v1.3.0 Installed Roots ─────────────────── v2.2.8 Installed BioGenerics ───────────── v0.1.5 Installed Distributions ─────────── v0.25.120 Installed InverseFunctions ──────── v0.1.17 Installed Reexport ──────────────── v1.2.2 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed SpecialFunctions ──────── v2.5.1 Installed Preferences ───────────── v1.4.3 Installed SortingAlgorithms ─────── v1.2.1 Installed PDMats ────────────────── v0.11.35 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.42 Installed VariantCallFormat ─────── v0.5.6 Installed Automa ────────────────── v0.8.4 Installed BGZFStreams ───────────── v0.3.2 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [66dad0bd] + AliasTables v1.1.3 ⌅ [67c07d97] + Automa v0.8.4 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [34da2185] + Compat v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.5 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.1 [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 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.8 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [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 v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 7.83s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4413.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 361.53s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_Zh6YV8/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [09f84164] HypothesisTests v0.11.5 [92933f4c] ProgressMeter v1.10.4 [276daf66] SpecialFunctions v2.5.1 [2913bbd2] StatsBase v0.34.5 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Zh6YV8/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [66dad0bd] AliasTables v1.1.3 ⌅ [67c07d97] Automa v0.8.4 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.17.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.5 [842dd82b] InlineStrings v1.4.4 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [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 v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.8 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.14.1+1 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.9s Test Summary: | Pass Total Time openvcf | 4 4 2.5s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.4s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.6s ┌ 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: 0:27:47 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 15.066201 seconds (10.61 M allocations: 665.598 MiB, 4.65% gc time, 96.31% compilation time: 25% of which was recompilation) 0.459205 seconds (2.86 M allocations: 195.909 MiB, 11.11% gc time, 18.45% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:24:38 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.619983 seconds (4.37 M allocations: 297.889 MiB, 3.25% gc time, 83.31% compilation time) 0.405175 seconds (2.85 M allocations: 195.465 MiB, 6.36% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 22.5s Test Summary: | Pass Total Time get sampleID | 4 4 0.0s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 2.0s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.1s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 6.8s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:40 Progress: 0%|▏ | ETA: 0:20:10 Progress: 0%|▏ | ETA: 0:19:59 Progress: 0%|▏ | ETA: 0:19:46 Progress: 0%|▏ | ETA: 0:19:27 Progress: 1%|▎ | ETA: 0:19:15 Progress: 1%|▎ | ETA: 0:19:09 Progress: 1%|▎ | ETA: 0:19:04 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records are matched 256.428546 seconds (2.19 G allocations: 143.741 GiB, 6.68% gc time, 0.58% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:23:59 Progress: 0%| | ETA: 0:23:50 Progress: 0%|▏ | ETA: 0:23:05 Progress: 0%|▏ | ETA: 0:22:33 Progress: 0%|▏ | ETA: 0:22:12 Progress: 0%|▏ | ETA: 0:21:59 Progress: 1%|▎ | ETA: 0:21:52 Progress: 1%|▎ | ETA: 0:21:48 Progress: 1%|▎ | ETA: 0:21:41 Progress: 1%|▍ | ETA: 0:21:38 Progress: 1%|▍ | ETA: 0:21:35 Progress: 1%|▍ | ETA: 0:21:33 Progress: 1%|▍ | ETA: 0:21:29 Progress: 1%|▌ | ETA: 0:21:26 Progress: 1%|▌ | ETA: 0:21:23 Progress: 1%|▌ | ETA: 0:21:22 Progress: 1%|▌ | ETA: 0:21:20 Progress: 1%|▋ | ETA: 0:21:19 Progress: 1%|▋ | ETA: 0:21:18 Progress: 2%|▋ | ETA: 0:21:16 Progress: 2%|▋ | ETA: 0:21:15 Progress: 2%|▊ | ETA: 0:21:16 Progress: 2%|▊ | ETA: 0:21:14 Progress: 2%|▊ | ETA: 0:21:13 Progress: 2%|▊ | ETA: 0:21:12 Progress: 2%|▉ | ETA: 0:21:07 Progress: 2%|▉ | ETA: 0:21:05 Progress: 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0:18:12 Progress: 8%|███▌ | ETA: 0:18:09 Progress: 9%|███▌ | ETA: 0:18:07 Progress: 9%|███▌ | ETA: 0:18:05 Progress: 9%|███▋ | ETA: 0:18:02 Progress: 9%|███▋ | ETA: 0:18:00 Progress: 9%|███▋ | ETA: 0:17:58 Progress: 9%|███▊ | ETA: 0:17:56 Progress: 9%|███▊ | ETA: 0:17:53 Progress: 9%|███▊ | ETA: 0:17:51 Progress: 9%|███▉ | ETA: 0:17:48 Progress: 9%|███▉ | ETA: 0:17:46 Progress: 10%|███▉ | ETA: 0:17:44 Progress: 10%|████ | ETA: 0:17:42 Progress: 10%|████ | ETA: 0:17:42 Progress: 10%|████ | ETA: 0:17:42 Progress: 10%|████ | ETA: 0:17:43 Progress: 10%|████▏ | ETA: 0:17:43 Progress: 10%|████▏ | ETA: 0:17:43 Progress: 10%|████▏ | ETA: 0:17:43 Progress: 10%|████▏ | ETA: 0:17:42 Progress: 10%|████▎ | ETA: 0:17:42 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 1 days, 0:28:12 Progress: 15%|██████ | ETA: 0:12:38 Progress: 31%|████████████▉ | ETA: 0:04:48 Progress: 48%|███████████████████▊ | ETA: 0:02:24 Progress: 65%|██████████████████████████▌ | ETA: 0:01:14 Progress: 82%|█████████████████████████████████▊ | ETA: 0:00:29 Progress: 99%|█████████████████████████████████████████| ETA: 0:00:00 Progress: 100%|█████████████████████████████████████████| Time: 0:02:16 [ Info: 0 records are matched 269.671405 seconds (2.19 G allocations: 143.725 GiB, 6.72% gc time, 0.37% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 13m35.6s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:49:22 Progress: 17%|██████▉ | ETA: 0:09:45 Progress: 35%|██████████████▎ | ETA: 0:03:40 Progress: 55%|██████████████████████▊ | ETA: 0:01:36 Progress: 76%|███████████████████████████████▏ | ETA: 0:00:38 Progress: 98%|████████████████████████████████████████▎| ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 833 records are matched 131.284369 seconds (1.11 G allocations: 72.817 GiB, 6.47% gc time, 0.50% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:24:31 Progress: 16%|██████▊ | ETA: 0:09:47 Progress: 33%|█████████████▊ | ETA: 0:03:50 Progress: 51%|████████████████████▊ | ETA: 0:01:54 Progress: 68%|████████████████████████████ | ETA: 0:00:55 Progress: 86%|███████████████████████████████████▎ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:59 [ Info: 493 records are matched 130.308759 seconds (1.11 G allocations: 72.816 GiB, 6.58% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:45:00 Progress: 24%|█████████▋ | ETA: 0:06:37 Progress: 54%|██████████████████████▏ | ETA: 0:01:45 Progress: 85%|██████████████████████████████████▋ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:02:04 [ Info: 0 records are matched 134.722135 seconds (1.11 G allocations: 72.817 GiB, 6.70% gc time, 0.54% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m38.7s 0.905454 seconds (1.28 M allocations: 91.351 MiB, 5.17% gc time, 89.31% compilation time) 0.870858 seconds (1.16 M allocations: 86.635 MiB, 4.28% gc time, 79.44% compilation time) 0.695073 seconds (1.16 M allocations: 85.881 MiB, 86.81% compilation time) 0.345517 seconds (203.61 k allocations: 11.563 MiB, 6.17% gc time, 99.94% compilation time) 0.009447 seconds (6.18 k allocations: 483.492 KiB, 96.53% compilation time) 0.010173 seconds (2.65 k allocations: 247.555 KiB, 96.37% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 7.6s 0.783402 seconds (952.91 k allocations: 74.538 MiB, 4.72% gc time, 81.84% compilation time) 0.659974 seconds (860.66 k allocations: 71.554 MiB, 86.67% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.1s Test Summary: | Pass Total Time convert_ds | 5 5 0.9s 0.161558 seconds (525.31 k allocations: 50.449 MiB, 51.69% gc time, 18.01% compilation time) 1.074297 seconds (647.60 k allocations: 57.720 MiB, 44.93% gc time, 49.09% compilation time: <1% of which was recompilation) ┌ 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 0.098622 seconds (520.43 k allocations: 51.916 MiB) 0.615633 seconds (589.76 k allocations: 56.017 MiB, 9.73% gc time, 77.78% 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 0.171215 seconds (1.56 M allocations: 81.839 MiB, 18.17% gc time, 5.92% compilation time) 0.683342 seconds (1.70 M allocations: 90.369 MiB, 82.46% 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 7.2s Test Summary: | Pass Total Time record info | 14 14 6.0s Test Summary: | Pass Total Time write VCF | 3 3 5.0s 2.968098 seconds (5.25 M allocations: 378.573 MiB, 22.08% gc time, 46.01% compilation time) 1.052449 seconds (2.86 M allocations: 194.731 MiB, 5.45% gc time, 23.06% compilation time) 0.961852 seconds (4.89 M allocations: 358.187 MiB, 8.00% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 7.8s 1.243838 seconds (618.95 k allocations: 54.420 MiB, 2.04% gc time, 47.12% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 3.6s Test Summary: | Pass Total Time filter_chr | 4 4 1.8s Progress: 0%|▏ | ETA: 0:26:24 Progress: 1%|▎ | ETA: 0:23:45 Progress: 1%|▌ | ETA: 0:23:27 Progress: 1%|▋ | ETA: 0:23:18 Progress: 2%|▊ | ETA: 0:23:17 Progress: 2%|▉ | ETA: 0:23:14 Progress: 2%|█ | ETA: 0:23:13 Progress: 3%|█▏ | ETA: 0:23:12 Progress: 3%|█▎ | ETA: 0:23:10 Progress: 4%|█▌ | ETA: 0:23:06 Progress: 4%|█▋ | ETA: 0:23:03 Progress: 4%|█▊ | ETA: 0:22:59 Progress: 5%|█▉ | ETA: 0:22:52 Progress: 5%|██ | ETA: 0:22:46 Progress: 5%|██▏ | ETA: 0:22:39 Progress: 6%|██▎ | ETA: 0:22:35 Progress: 6%|██▌ | ETA: 0:22:32 Progress: 6%|██▋ | ETA: 0:22:27 Progress: 7%|██▊ | ETA: 0:22:22 Progress: 7%|██▉ | ETA: 0:22:18 Progress: 7%|███ | ETA: 0:22:14 Progress: 8%|███▏ | ETA: 0:22:11 Progress: 8%|███▎ | ETA: 0:22:07 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63%|█████████████████████████▊ | ETA: 0:08:50 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 428 running 1 of 1 signal (10): User defined signal 1 ijl_isa at /source/src/subtype.c:2481 ijl_typeassert at /source/src/rtutils.c:235 _deepcopy_memory_t at ./deepcopy.jl:120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/YgfJC/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x70c612d18356) at (unknown file) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_invoke at /source/src/gf.c:3814 jl_toplevel_eval_flex at /source/src/toplevel.c:762 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_34655.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_34655.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 exec_options at ./client.jl:286 _start at ./client.jl:553 jfptr__start_42579.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x70c635222249) 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) Progress: 63%|█████████████████████████▉ | ETA: 0:08:45 ============================================================== Profile collected. A report will print at the next yield point ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_52533.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== Progress: 64%|██████████████████████████▏ | ETA: 0:08:40┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000078bba8e07850 Total snapshots: 303. Utilization: 0% ╎303 @Base/task.jl:1129 wait_forever() 302╎ 303 @Base/task.jl:1192 wait() ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000070c61b000010 Total snapshots: 541. Utilization: 100% ╎540 @Base/client.jl:553 _start() ╎ 540 @Base/client.jl:286 exec_options(opts::Base.JLOptions) ╎ 540 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 540 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 540 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 540 @Base/loading.jl:2908 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 540 @Base/loading.jl:2848 include_string(mapexpr::typeof(identity), m… ╎ ╎ 540 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 540 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ ╎ 540 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 540 @Base/loading.jl:2908 _include(mapexpr::Function, mod::Module… ╎ ╎ ╎ 540 @Base/loading.jl:2848 include_string(mapexpr::typeof(identit… ╎ ╎ ╎ 540 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ 540 @VCFTools/…_test.jl:3 top-level scope ╎ ╎ ╎ 540 @Test/src/Test.jl:1858 macro expansion ╎ ╎ ╎ 540 @VCFTools/…test.jl:19 macro expansion ╎ ╎ ╎ ╎ 540 @VCFTools/…lect.jl:26 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 71 @VCFTools/…ect.jl:44 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 25 @VCFTools/…ect.jl:65 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 25 @VCFTools/…ts.jl:122 gtstats ╎ ╎ ╎ ╎ 22 @VCFTools/…ts.jl:127 gtstats(record::VariantCallFor… 8╎ ╎ ╎ ╎ ╎ 8 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 6 @Base/…ators.jl:425 > 6╎ ╎ ╎ ╎ ╎ 6 @Base/int.jl:83 < ╎ ╎ ╎ ╎ ╎ 8 @VCFTools/…t.jl:225 geno_ismissing ╎ ╎ ╎ ╎ ╎ 6 @Base/…tials.jl:966 getindex 1╎ ╎ ╎ ╎ ╎ 6 @Base/…ials.jl:387 checkbounds ╎ ╎ ╎ ╎ ╎ 5 @Base/…ials.jl:383 checkbounds 5╎ ╎ ╎ ╎ ╎ 5 @Base/…ials.jl:11 length 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:967 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == ╎ ╎ ╎ ╎ 1 @VCFTools/…ts.jl:133 gtstats(record::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:383 checkbounds ╎ ╎ ╎ ╎ 2 @VCFTools/…ts.jl:134 gtstats(record::VariantCallFor… 2╎ ╎ ╎ ╎ ╎ 2 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 39 @VCFTools/…ect.jl:74 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 38 @Base/array.jl:2458 findfirst 1╎ ╎ ╎ ╎ 36 @Base/array.jl:2407 findnext 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ ╎ 34 @Base/…ators.jl:1195 Fix ╎ ╎ ╎ ╎ ╎ 34 @Base/…tors.jl:1195 #_#59 ╎ ╎ ╎ ╎ ╎ 34 @Base/…tors.jl:178 isequal 34╎ ╎ ╎ ╎ ╎ 34 @Base/…ring.jl:186 == ╎ ╎ ╎ ╎ 2 @Base/array.jl:2408 findnext 2╎ ╎ ╎ ╎ ╎ 2 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 3 @VCFTools/…ect.jl:76 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 findgenokey ╎ ╎ ╎ ╎ 3 @Base/array.jl:2458 findfirst ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:2407 findnext ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:613 #findgenokey##0 ╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:673 isequaldata 3╎ ╎ ╎ ╎ ╎ 3 @VariantCallFormat/…:677 memcmp ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:79 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 1 @Base/…rators.jl:425 > 1╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ 1 @VCFTools/…rt.jl:225 geno_ismissing 1╎ ╎ ╎ ╎ 1 @Base/…mpiler.jl:57 getproperty ╎ ╎ ╎ ╎ 2 @VCFTools/…ect.jl:99 aim_select(record::VariantCallFo… ╎ ╎ ╎ ╎ 2 @Base/…al/log.jl:261 log(x::Float64) ╎ ╎ ╎ ╎ 2 @Base/…al/log.jl:289 _log ╎ ╎ ╎ ╎ ╎ 2 @Base/…l/log.jl:163 log_proc1 2╎ ╎ ╎ ╎ ╎ 2 @Base/float.jl:492 + ╎ ╎ ╎ ╎ 1 @VCFTools/…ect.jl:45 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:483 next! ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:484 #next!#15 ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:470 lock_if_threading ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:486 #17 ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:211 updateProgress! ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:213 #updateProgress!#9 ╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:217 _updateProgress! 1╎ ╎ ╎ ╎ ╎ 1 @ProgressMeter/…:0 _updateProgress!(p::Progres… ╎ ╎ ╎ ╎ 468 @VCFTools/…ect.jl:46 aim_select(vcffile::String, sampl… ╎ ╎ ╎ ╎ 468 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 66 @BioGenerics/…jl:87 iterate 1╎ ╎ ╎ ╎ 1 @BioGenerics/…jl:75 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ 65 @BioGenerics/…jl:76 tryread!(reader::VariantCallFor… ╎ ╎ ╎ ╎ ╎ 65 @VariantCallFormat/…:147 read!(reader::VariantCall… ╎ ╎ ╎ ╎ ╎ 61 @VariantCallFormat/…:169 _read!(reader::VariantCa… 2╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:0 macro expansion 1╎ ╎ ╎ ╎ ╎ 1 @Automa/…en.jl:0 macro expansion ╎ ╎ ╎ ╎ ╎ 55 @Automa/…en.jl:263 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:425 lastindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…rray.jl:390 eachindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:11 length ╎ ╎ ╎ ╎ ╎ 20 @Base/array.jl:411 getindex 20╎ ╎ ╎ ╎ ╎ 20 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ ╎ 31 @Base/array.jl:1303 push! ╎ ╎ ╎ ╎ ╎ 29 @Base/…ray.jl:1306 _push! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1168 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:11 length ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:1172 _growend! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - 1╎ ╎ ╎ ╎ ╎ ╎ 27 @Base/…ray.jl:1174 _growend! ╎ ╎ ╎ ╎ ╎ ╎ 20 @Base/…ay.jl:1149 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ ╎ 20 @Base/…ay.jl:1069 array_new_memory 20╎ ╎ ╎ ╎ ╎ ╎ 20 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1152 _growend_internal!(a::Vect… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ot.jl:595 memoryref 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:1157 _growend_internal!(a::Vect… 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…ay.jl:1158 _growend_internal!(a::Vect… ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1307 _push! 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ray.jl:1012 __safe_setindex! 3╎ ╎ ╎ ╎ ╎ 3 @Base/…ials.jl:967 getindex 2╎ ╎ ╎ ╎ ╎ 3 @Automa/…en.jl:292 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/range.jl:1452 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/bool.jl:40 & ╎ ╎ ╎ ╎ ╎ 4 @VariantCallFormat/…:185 _read!(reader::VariantCa… ╎ ╎ ╎ ╎ ╎ 4 @BufferedStreams/…:61 fillbuffer! ╎ ╎ ╎ ╎ ╎ 4 @BufferedStreams/…:71 fillbuffer! ╎ ╎ ╎ ╎ ╎ 4 @BufferedStreams/…:5 readbytes! ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:387 readbytes!(stream::… ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:201 eof(stream::Transc… ╎ ╎ ╎ ╎ ╎ ╎ 3 @TranscodingStreams/…:582 fillbuffer ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:594 fillbuffer(strea… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:128 makemargin! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:147 makemargin!(bu… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:299 copyto! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:308 _copyto_impl! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ry.jl:125 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:596 fillbuffer(strea… ╎ ╎ ╎ ╎ ╎ ╎ 2 @TranscodingStreams/…:656 callprocess(str… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:195 process(codec::GzipDeco… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @CodecZlib/…:127 inflate! ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:392 readbytes!(stream::… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:26 unsafe_read(input::… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:371 unsafe_read(strea… ╎ ╎ ╎ ╎ ╎ ╎ 1 @TranscodingStreams/…:213 copydata! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:268 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ 402 @BioGenerics/…jl:90 iterate ╎ ╎ ╎ ╎ 402 @VariantCallFormat/…:309 copy(record::VariantCallFo… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:360 copy 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ 401 @Base/…pcopy.jl:34 deepcopy ╎ ╎ ╎ ╎ ╎ 1 @Base/…pcopy.jl:129 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tdict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:182 in 1╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:92 get ╎ ╎ ╎ ╎ ╎ 400 @Base/…pcopy.jl:133 deepcopy_internal(x::Vector{V… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:138 deepcopy_internal(x::MemoryRe… ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:182 in 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…dict.jl:92 get ╎ ╎ ╎ ╎ ╎ 399 @Base/…copy.jl:142 deepcopy_internal(x::MemoryRe… 2╎ ╎ ╎ ╎ ╎ 399 @Base/…copy.jl:104 deepcopy_internal 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:0 _deepcopy_memory_t(x::Memory,… ╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:108 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:864 isbitstype ╎ ╎ ╎ ╎ ╎ 2 @Base/…copy.jl:111 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:588 GenericMemory 51╎ ╎ ╎ ╎ ╎ 51 @Base/…copy.jl:116 _deepcopy_memory_t(x::Memor… 17╎ ╎ ╎ ╎ ╎ 17 @Base/…copy.jl:117 _deepcopy_memory_t(x::Memor… 7╎ ╎ ╎ ╎ ╎ 7 @Base/…copy.jl:118 _deepcopy_memory_t(x::Memor… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…copy.jl:119 _deepcopy_memory_t(x::Memor… 16╎ ╎ ╎ ╎ ╎ 271 @Base/…copy.jl:120 _deepcopy_memory_t(x::Memor… 2╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…opy.jl:0 deepcopy_internal(x::Vector{U… ╎ ╎ ╎ ╎ ╎ ╎ 18 @Base/…opy.jl:129 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 18 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 18 @Base/…ct.jl:182 in 18╎ ╎ ╎ ╎ ╎ ╎ 18 @Base/…ct.jl:92 get ╎ ╎ ╎ ╎ ╎ ╎ 48 @Base/…opy.jl:132 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/boot.jl:661 Array 14╎ ╎ ╎ ╎ ╎ ╎ 14 @Base/…ot.jl:649 Array 33╎ ╎ ╎ ╎ ╎ ╎ 34 @Base/…ict.jl:86 setindex! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ler.jl:61 setproperty! 8╎ ╎ ╎ ╎ ╎ ╎ 179 @Base/…opy.jl:133 deepcopy_internal(x::Vector… ╎ ╎ ╎ ╎ ╎ ╎ 58 @Base/…opy.jl:138 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 58 @Base/…ict.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 58 @Base/…ct.jl:182 in 56╎ ╎ ╎ ╎ ╎ ╎ 58 @Base/…ct.jl:92 get 1╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…er.jl:57 getproperty ╎ ╎ ╎ ╎ ╎ ╎ 113 @Base/…opy.jl:142 deepcopy_internal(x::Memor… ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…py.jl:101 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ct.jl:19 haskey ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ct.jl:182 in 17╎ ╎ ╎ ╎ ╎ ╎ ╎ 17 @Base/…ct.jl:92 get 6╎ ╎ ╎ ╎ ╎ ╎ 96 @Base/…py.jl:104 deepcopy_internal 4╎ ╎ ╎ ╎ ╎ ╎ 4 @Base/…py.jl:107 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:108 _deepcopy_memory_t(x::Mem… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:864 isbitstype 19╎ ╎ ╎ ╎ ╎ ╎ 85 @Base/…py.jl:109 _deepcopy_memory_t(x::Mem… ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ry.jl:179 copy(a::Memory{UnitRange… 11╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ot.jl:588 GenericMemory ╎ ╎ ╎ ╎ ╎ ╎ 19 @Base/…ry.jl:180 copy(a::Memory{UnitRange… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 19 @Base/…ry.jl:143 unsafe_copyto! 8╎ ╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…ot.jl:595 memoryref ╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…ry.jl:125 unsafe_copyto! 11╎ ╎ ╎ ╎ ╎ ╎ ╎ 11 @Base/…em.jl:28 memmove 32╎ ╎ ╎ ╎ ╎ ╎ 34 @Base/…ct.jl:86 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:61 setproperty! ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…ct.jl:87 setindex! 2╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…er.jl:61 setproperty! 8╎ ╎ ╎ ╎ ╎ ╎ 8 @Base/…opy.jl:134 deepcopy_internal(x::Vector… 35╎ ╎ ╎ ╎ ╎ 35 @Base/…copy.jl:122 _deepcopy_memory_t(x::Memor… 11╎ ╎ ╎ ╎ ╎ 11 @Base/…copy.jl:123 _deepcopy_memory_t(x::Memor… [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 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_52533.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 22199007 (Pool: 22198416; Big: 591); GC: 23 [428] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:1 ijl_eqtable_get at /source/src/iddict.c:159 get at ./iddict.jl:92 [inlined] in at ./iddict.jl:182 [inlined] haskey at ./abstractdict.jl:19 [inlined] deepcopy_internal at ./deepcopy.jl:101 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 unknown function (ip: 0x70c633eed446) at (unknown file) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 _deepcopy_memory_t at ./deepcopy.jl:120 deepcopy_internal at ./deepcopy.jl:104 [inlined] deepcopy_internal at ./deepcopy.jl:142 deepcopy_internal at ./deepcopy.jl:133 deepcopy at ./deepcopy.jl:34 [inlined] copy at /home/pkgeval/.julia/packages/VariantCallFormat/YgfJC/src/record.jl:309 iterate at /home/pkgeval/.julia/packages/BioGenerics/53MtO/src/IO.jl:90 [inlined] iterate at ./iterators.jl:197 [inlined] aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:46 aim_select at /home/pkgeval/.julia/packages/VCFTools/IWkMe/src/aim_select.jl:26 unknown function (ip: 0x70c612d18356) at (unknown file) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 macro expansion at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:19 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] top-level scope at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/aim_test.jl:3 _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_invoke at /source/src/gf.c:3814 jl_toplevel_eval_flex at /source/src/toplevel.c:762 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_34655.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 include_string at ./loading.jl:2848 _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 _include at ./loading.jl:2908 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_34655.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:708 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:773 jl_toplevel_eval_flex at /source/src/toplevel.c:713 ijl_toplevel_eval at /source/src/toplevel.c:785 ijl_toplevel_eval_in at /source/src/toplevel.c:830 eval at ./boot.jl:489 exec_options at ./client.jl:286 _start at ./client.jl:553 jfptr__start_42579.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x70c635222249) 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: 16779570909 (Pool: 16779555421; Big: 15488); GC: 29837 PkgEval terminated after 2727.79s: test duration exceeded the time limit