Package evaluation to test VCFTools on Julia 1.14.0-DEV.1491 (0e7d18362a*) started at 2026-01-11T13:04:51.703 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.27s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.43 [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 v1.1.0 [38540f10] + CommonSolve v0.2.6 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.15.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [4c63d2b9] + StatsFuns v1.5.2 [3bb67fe8] + TranscodingStreams v0.11.3 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [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 v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 5.44s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 13.59s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_b7PkhM/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.9 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [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_b7PkhM/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [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 v1.1.0 [38540f10] CommonSolve v0.2.6 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [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 [ca575930] NetworkOptions v1.3.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v8.17.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 2.7s Test Summary: | Pass Total Time openvcf | 4 4 1.9s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 1.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.3s ┌ 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: 0:24:43 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 11.759659 seconds (9.82 M allocations: 559.093 MiB, 5.81% gc time, 95.60% compilation time: 20% of which was recompilation) 0.373824 seconds (2.37 M allocations: 141.367 MiB, 8.37% gc time, 15.25% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:20:39 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.692419 seconds (4.02 M allocations: 238.973 MiB, 19.76% gc time, 68.32% compilation time: <1% of which was recompilation) 0.397659 seconds (2.37 M allocations: 141.297 MiB, 2.58% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 18.2s Test Summary: | Pass Total Time get sampleID | 4 4 0.1s Test Summary: | Pass Total Time Fishers exact HWE test | 20 20 0.0s Test Summary: | Pass Total Time filter_genotype(record) | 9 9 1.1s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 1.9s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.7s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.7s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:22 Progress: 0%|▏ | ETA: 0:22:48 Progress: 0%|▏ | ETA: 0:20:03 Progress: 0%|▏ | ETA: 0:20:44 Progress: 0%|▎ | ETA: 0:19:31 Progress: 1%|▎ | ETA: 0:18:48 Progress: 1%|▎ | ETA: 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Progress: 64%|██████████████████████████▏ | ETA: 0:00:56 Progress: 84%|██████████████████████████████████▋ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:01:40 [ Info: 823 records are matched 221.697135 seconds (2.01 G allocations: 106.140 GiB, 18.79% gc time, 0.49% compilation time: 8% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:10 Progress: 0%|▏ | ETA: 0:21:16 Progress: 0%|▏ | ETA: 0:19:26 Progress: 0%|▏ | ETA: 0:19:00 Progress: 1%|▎ | ETA: 0:16:55 Progress: 1%|▎ | ETA: 0:16:40 Progress: 1%|▍ | ETA: 0:15:40 Progress: 1%|▍ | ETA: 0:15:32 Progress: 1%|▌ | ETA: 0:14:54 Progress: 1%|▌ | ETA: 0:14:28 Progress: 1%|▋ | ETA: 0:14:33 Progress: 2%|▋ | ETA: 0:14:34 Progress: 2%|▊ | ETA: 0:15:00 Progress: 2%|▊ | ETA: 0:14:57 Progress: 2%|▊ | ETA: 0:14:59 Progress: 2%|▉ | ETA: 0:15:24 Progress: 2%|▉ | ETA: 0:15:25 Progress: 2%|▉ | ETA: 0:15:26 Progress: 2%|█ | ETA: 0:15:27 Progress: 2%|█ | ETA: 0:15:47 Progress: 3%|█ 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Progress: 9%|███▉ | ETA: 0:15:55 Progress: 9%|███▉ | ETA: 0:15:58 Progress: 10%|███▉ | ETA: 0:15:55 Progress: 10%|████ | ETA: 0:15:52 Progress: 10%|████ | ETA: 0:15:52 Progress: 10%|████ | ETA: 0:15:50 Progress: 10%|████▏ | ETA: 0:15:47 Progress: 10%|████▏ | ETA: 0:15:46 Progress: 10%|████▎ | ETA: 0:15:44 Progress: 10%|████▎ | ETA: 0:15:42 Progress: 100%|█████████████████████████████████████████| Time: 0:01:48 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:36:55 Progress: 19%|███████▋ | ETA: 0:08:04 Progress: 39%|████████████████▏ | ETA: 0:02:53 Progress: 60%|████████████████████████▌ | ETA: 0:01:16 Progress: 83%|██████████████████████████████████▏ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 488 records are matched 234.298263 seconds (2.01 G allocations: 106.121 GiB, 18.22% gc time, 0.30% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:16:11 Progress: 0%|▏ | ETA: 0:19:33 Progress: 0%|▏ | 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100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 20:46:18 Progress: 11%|████▋ | ETA: 0:14:49 Progress: 33%|█████████████▋ | ETA: 0:03:46 Progress: 55%|██████████████████████▋ | ETA: 0:01:32 Progress: 77%|███████████████████████████████▋ | ETA: 0:00:34 Progress: 99%|████████████████████████████████████████▊| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:01:56 [ Info: 0 records are matched 238.007275 seconds (2.01 G allocations: 106.121 GiB, 17.98% gc time, 0.18% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m40.9s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:17:14 Progress: 19%|███████▊ | ETA: 0:07:50 Progress: 39%|███████████████▉ | ETA: 0:02:53 Progress: 59%|████████████████████████▏ | ETA: 0:01:18 Progress: 81%|█████████████████████████████████▎ | ETA: 0:00:26 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: 833 records are matched 123.786449 seconds (1.02 G allocations: 53.885 GiB, 16.06% gc time, 0.38% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:32:11 Progress: 20%|████████▏ | ETA: 0:07:25 Progress: 41%|████████████████▊ | ETA: 0:02:42 Progress: 62%|█████████████████████████▎ | ETA: 0:01:10 Progress: 85%|██████████████████████████████████▊ | ETA: 0:00:20 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 493 records are matched 125.159956 seconds (1.02 G allocations: 53.885 GiB, 16.39% gc time, 0.35% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:31:13 Progress: 18%|███████▌ | ETA: 0:08:09 Progress: 39%|████████████████ | ETA: 0:02:55 Progress: 59%|████████████████████████▎ | ETA: 0:01:18 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 0 records are matched 125.031627 seconds (1.02 G allocations: 53.884 GiB, 16.25% gc time, 0.41% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m16.0s 0.965329 seconds (1.26 M allocations: 68.077 MiB, 85.12% compilation time) 0.873033 seconds (1.16 M allocations: 64.743 MiB, 3.37% gc time, 78.67% compilation time) 0.763327 seconds (1.16 M allocations: 63.777 MiB, 82.47% compilation time) 0.386058 seconds (207.71 k allocations: 10.883 MiB, 99.96% compilation time) 0.011618 seconds (6.46 k allocations: 398.680 KiB, 97.31% compilation time) 0.010590 seconds (2.65 k allocations: 165.445 KiB, 97.40% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 7.0s 0.696720 seconds (1.04 M allocations: 58.258 MiB, 5.04% gc time, 80.97% compilation time) 0.693105 seconds (884.43 k allocations: 52.065 MiB, 3.72% gc time, 76.82% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 4.3s Test Summary: | Pass Total Time convert_ds | 5 5 0.9s 0.112494 seconds (525.74 k allocations: 30.690 MiB, 18.39% gc time, 36.17% compilation time) 0.497431 seconds (647.59 k allocations: 37.462 MiB, 89.22% 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 0.491158 seconds (520.59 k allocations: 32.160 MiB, 90.15% gc time) 0.318258 seconds (597.97 k allocations: 36.535 MiB, 85.06% 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 0.096943 seconds (1.56 M allocations: 62.080 MiB, 9.72% compilation time) 0.540611 seconds (1.71 M allocations: 70.407 MiB, 6.24% gc time, 70.53% 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 4.8s Test Summary: | Pass Total Time record info | 14 14 3.8s Test Summary: | Pass Total Time write VCF | 3 3 2.6s 1.809561 seconds (4.80 M allocations: 296.585 MiB, 4.38% gc time, 51.79% compilation time) 0.940756 seconds (2.39 M allocations: 142.661 MiB, 4.13% gc time, 21.47% compilation time) 0.863789 seconds (4.42 M allocations: 276.456 MiB, 6.70% gc time) Test Summary: | Pass Total Time filter by sample/record index | 9 9 6.1s 0.842564 seconds (606.37 k allocations: 33.463 MiB, 1.93% gc time, 37.46% compilation time) Test Summary: | Pass Total Time mask_gt | 5 5 2.9s Test Summary: | Pass Total Time filter_chr | 4 4 1.5s Progress: 0%|▎ | ETA: 0:20:24 Progress: 1%|▍ | ETA: 0:19:30 Progress: 1%|▌ | ETA: 0:19:46 Progress: 2%|▊ | ETA: 0:19:44 Progress: 2%|▉ | ETA: 0:19:32 Progress: 3%|█▏ | ETA: 0:19:39 Progress: 3%|█▎ | ETA: 0:19:24 Progress: 3%|█▍ | ETA: 0:19:28 Progress: 4%|█▋ | ETA: 0:19:31 Progress: 4%|█▊ | ETA: 0:19:20 Progress: 5%|██ | ETA: 0:19:22 Progress: 5%|██▏ | ETA: 0:19:13 Progress: 6%|██▎ | ETA: 0:19:10 Progress: 6%|██▌ | ETA: 0:19:10 Progress: 6%|██▋ | ETA: 0:19:00 Progress: 7%|██▉ | ETA: 0:18:58 Progress: 7%|███ | ETA: 0:18:57 Progress: 8%|███▏ | ETA: 0:18:48 Progress: 8%|███▍ | ETA: 0:18:47 Progress: 9%|███▌ | ETA: 0:18:41 Progress: 9%|███▊ | ETA: 0:18:31 Progress: 9%|███▉ | ETA: 0:18:25 Progress: 10%|████▏ | ETA: 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