Package evaluation to test VCFTools on Julia 1.14.0-DEV.2086 (d19eac062f*) started at 2026-04-28T19:57:43.473 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.54s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed CommonSolve ───────────── v0.2.6 Installed DelimitedFiles ────────── v1.9.1 Installed FillArrays ────────────── v1.16.0 Installed DataStructures ────────── v0.19.4 Installed MacroTools ────────────── v0.5.16 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed VCFTools ──────────────── v0.2.10 Installed CodecZlib ─────────────── v0.7.8 Installed StatsBase ─────────────── v0.34.10 Installed TranscodingStreams ────── v0.11.3 Installed OrderedCollections ────── v1.8.1 Installed HypergeometricFunctions ─ v0.3.28 Installed Combinatorics ─────────── v1.1.0 Installed DataAPI ───────────────── v1.16.0 Installed StatsAPI ──────────────── v1.8.0 Installed Statistics ────────────── v1.11.1 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed SIMD ──────────────────── v3.7.2 Installed HypothesisTests ───────── v0.11.7 Installed ProgressMeter ─────────── v1.11.0 Installed IrrationalConstants ───── v0.2.6 Installed QuadGK ────────────────── v2.11.3 Installed LogExpFunctions ───────── v0.3.29 Installed PrecompileTools ───────── v1.3.3 Installed BufferedStreams ───────── v1.2.2 Installed Rmath ─────────────────── v0.9.0 Installed Roots ─────────────────── v3.0.0 Installed PtrArrays ─────────────── v1.4.0 Installed BioGenerics ───────────── v0.1.5 Installed StatsFuns ─────────────── v1.5.2 Installed SpecialFunctions ──────── v2.7.2 Installed Distributions ─────────── v0.25.125 Installed Reexport ──────────────── v1.2.2 Installed InverseFunctions ──────── v0.1.17 Installed JLLWrappers ───────────── v1.7.1 Installed Missings ──────────────── v1.2.0 Installed PDMats ────────────────── v0.11.37 Installed SortingAlgorithms ─────── v1.2.2 Installed DocStringExtensions ───── v0.9.5 Installed Preferences ───────────── v1.5.2 Installed BGZFStreams ───────────── v0.3.2 Installed Automa ────────────────── v1.1.0 Installed Accessors ─────────────── v0.1.44 Installed VariantCallFormat ─────── v0.5.9 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.44 [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 v0.19.4 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.125 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.7 [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 v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.0 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.2 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [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 v1.5.1+0 [4536629a] + OpenBLAS_jll v0.3.32+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 9.35s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5.3 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 4.4 s ✓ MacroTools 1.8 s ✓ InlineStrings 0.8 s ✓ Reexport 1.2 s ✓ Statistics 0.9 s ✓ DataAPI 1.2 s ✓ ConstructionBase 2.3 s ✓ IrrationalConstants 0.8 s ✓ DataValueInterfaces 0.9 s ✓ StatsAPI 1.7 s ✓ OrderedCollections 1.1 s ✓ InvertedIndices 1.2 s ✓ InverseFunctions 1.1 s ✓ CompositionsBase 1.7 s ✓ DocStringExtensions 2.9 s ✓ Combinatorics 1.3 s ✓ WorkerUtilities 2.8 s ✓ FillArrays 1.3 s ✓ BufferedStreams 1.1 s ✓ PtrArrays 1.2 s ✓ CommonSolve 1.7 s ✓ TranscodingStreams 1.0 s ✓ IteratorInterfaceExtensions 1.1 s ✓ LaTeXStrings 2.6 s ✓ Crayons 1.3 s ✓ DelimitedFiles 2.5 s ✓ PDMats 3.2 s ✓ ProgressMeter 3.3 s ✓ SentinelArrays 1.5 s ✓ Compat 1.9 s ✓ Preferences 1.8 s ✓ Statistics → SparseArraysExt 1.3 s ✓ Missings 1.3 s ✓ PooledArrays 1.0 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 4.7 s ✓ DataStructures 2.5 s ✓ InverseFunctions → InverseFunctionsTestExt 1.6 s ✓ InverseFunctions → InverseFunctionsDatesExt 1.0 s ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1.8 s ✓ LogExpFunctions 2.0 s ✓ FillArrays → FillArraysSparseArraysExt 1.4 s ✓ FillArrays → FillArraysStatisticsExt 1.4 s ✓ AliasTables 1.2 s ✓ BioGenerics 1.4 s ✓ CodecZlib 1.0 s ✓ TableTraits 1.9 s ✓ FillArrays → FillArraysPDMatsExt 1.1 s ✓ Compat → CompatLinearAlgebraExt 2.0 s ✓ JLLWrappers 1.7 s ✓ PrecompileTools 1.5 s ✓ SortingAlgorithms 3.2 s ✓ QuadGK 7.4 s ✓ Accessors 1.1 s ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1.4 s ✓ BGZFStreams 2.5 s ✓ Tables 3.3 s ✓ FilePathsBase 3.0 s ✓ Rmath_jll 3.0 s ✓ OpenSpecFun_jll 5.3 s ✓ StringManipulation 20.3 s ✓ SIMD 23.9 s ✓ Parsers 5.9 s ✓ StatsBase 3.5 s ✓ Accessors → LinearAlgebraExt 3.1 s ✓ Accessors → TestExt 4.2 s ✓ FilePathsBase → FilePathsBaseTestExt 1.7 s ✓ FilePathsBase → FilePathsBaseMmapExt 2.4 s ✓ Rmath 7.2 s ✓ SpecialFunctions 59.3 s ✓ PrettyTables 26.9 s ✓ Automa 1.9 s ✓ InlineStrings → ParsersExt 1.9 s ✓ PDMats → StatsBaseExt 10.1 s ✓ Roots 3.4 s ✓ HypergeometricFunctions 121.1 s ✓ DataFrames [ Info: Compiling VCF parser... 22.6 s ✓ VariantCallFormat 4.2 s ✓ WeakRefStrings 4.3 s ✓ StatsFuns 36.1 s ✓ CSV 1.7 s ✓ StatsFuns → StatsFunsInverseFunctionsExt 11.7 s ✓ Distributions 5.3 s ✓ Distributions → DistributionsTestExt 5.6 s ✓ HypothesisTests 7.1 s ✓ VCFTools 84 dependencies successfully precompiled in 511 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 548.34s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_rCDT2L/Project.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.125 [09f84164] HypothesisTests v0.11.7 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.7.2 [2913bbd2] StatsBase v0.34.10 [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_rCDT2L/Manifest.toml` [7d9f7c33] Accessors v0.1.44 [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 v0.10.16 [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 v1.8.2 [864edb3b] DataStructures v0.19.4 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.125 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.7 [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 v2.8.4 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.0 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.2 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.4 [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 v1.4.3 [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 v1.5.1+0 [deac9b47] LibCURL_jll v8.19.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.32+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.6+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 4.0s Test Summary: | Pass Total Time openvcf | 4 4 3.2s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 3.4s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 5.0s ┌ 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: 0:53:40 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 17.983264 seconds (9.13 M allocations: 553.160 MiB, 2.02% gc time, 95.11% compilation time: 16% of which was recompilation) 0.479248 seconds (2.37 M allocations: 141.369 MiB, 13.13% gc time, 17.02% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:49:43 Progress: 75%|██████████████████████████████▋ | ETA: 0:00:02 Progress: 100%|█████████████████████████████████████████| Time: 0:00:05 5.544212 seconds (3.95 M allocations: 239.914 MiB, 13.21% gc time, 79.72% compilation time: <1% of which was recompilation) 0.486019 seconds (2.37 M allocations: 141.118 MiB, 4.39% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 29.3s 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 2.4s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.2s Test Summary: | Pass Total Time flip_gt_allele | 4 4 1.3s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.5s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:51 Progress: 0%|▏ | ETA: 0:20:06 Progress: 0%|▏ | ETA: 0:24:13 Progress: 0%|▏ | ETA: 0:23:16 Progress: 0%|▏ | ETA: 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| ETA: 0:17:18 Progress: 6%|██▌ | ETA: 0:17:15 Progress: 6%|██▌ | ETA: 0:17:13 Progress: 6%|██▋ | ETA: 0:17:10 Progress: 6%|██▋ | ETA: 0:17:14 Progress: 6%|██▋ | ETA: 0:17:11 Progress: 7%|██▊ | ETA: 0:17:07 Progress: 7%|██▊ | ETA: 0:17:04 Progress: 7%|██▊ | ETA: 0:17:00 Progress: 7%|██▉ | ETA: 0:16:57 Progress: 7%|██▉ | ETA: 0:17:01 Progress: 7%|██▉ | ETA: 0:16:57 Progress: 7%|███ | ETA: 0:16:55 Progress: 7%|███ | ETA: 0:16:53 Progress: 7%|███ | ETA: 0:16:50 Progress: 8%|███▏ | ETA: 0:16:55 Progress: 8%|███▏ | ETA: 0:16:53 Progress: 8%|███▏ | ETA: 0:16:51 Progress: 8%|███▎ | ETA: 0:16:49 Progress: 8%|███▎ | ETA: 0:16:48 Progress: 8%|███▎ | ETA: 0:16:51 Progress: 8%|███▍ | ETA: 0:16:49 Progress: 8%|███▍ | ETA: 0:16:47 Progress: 8%|███▍ | ETA: 0:16:45 Progress: 8%|███▌ | ETA: 0:16:43 Progress: 9%|███▌ | ETA: 0:16:42 Progress: 9%|███▌ | ETA: 0:16:44 Progress: 9%|███▋ | ETA: 0:16:42 Progress: 9%|███▋ | ETA: 0:16:39 Progress: 9%|███▋ | ETA: 0:16:37 Progress: 9%|███▊ | ETA: 0:16:35 Progress: 9%|███▊ | ETA: 0:16:38 Progress: 9%|███▊ | ETA: 0:16:36 Progress: 9%|███▉ | ETA: 0:16:34 Progress: 9%|███▉ | ETA: 0:16:31 Progress: 10%|███▉ | ETA: 0:16:29 Progress: 10%|████ | ETA: 0:16:32 Progress: 10%|████ | ETA: 0:16:31 Progress: 10%|████ | ETA: 0:16:29 Progress: 10%|████▏ | ETA: 0:16:26 Progress: 10%|████▏ | ETA: 0:16:24 Progress: 10%|████▏ | ETA: 0:16:27 Progress: 10%|████▎ | ETA: 0:16:26 Progress: 100%|█████████████████████████████████████████| Time: 0:01:53 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 21:08:00 Progress: 21%|████████▊ | ETA: 0:07:00 Progress: 42%|█████████████████▎ | ETA: 0:02:37 Progress: 61%|█████████████████████████ | ETA: 0:01:14 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:22 Progress: 100%|█████████████████████████████████████████| Time: 0:01:58 [ Info: 0 records are matched 241.765092 seconds (2.01 G allocations: 106.049 GiB, 12.52% gc time, 0.40% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m42.9s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:46:39 Progress: 20%|████████▏ | ETA: 0:07:33 Progress: 39%|████████████████▏ | ETA: 0:02:54 Progress: 59%|████████████████████████ | ETA: 0:01:21 Progress: 81%|█████████████████████████████████▏ | ETA: 0:00:27 Progress: 100%|█████████████████████████████████████████| Time: 0:01:55 [ Info: 833 records are matched 126.020553 seconds (1.01 G allocations: 53.815 GiB, 10.86% gc time, 0.50% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:34:42 Progress: 20%|████████▎ | ETA: 0:07:22 Progress: 41%|████████████████▉ | ETA: 0:02:38 Progress: 62%|█████████████████████████▍ | ETA: 0:01:10 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: 493 records are matched 124.827729 seconds (1.01 G allocations: 53.814 GiB, 11.03% gc time, 0.52% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:34:03 Progress: 19%|███████▉ | ETA: 0:07:49 Progress: 37%|███████████████ | ETA: 0:03:14 Progress: 59%|████████████████████████▏ | ETA: 0:01:19 Progress: 83%|██████████████████████████████████ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:54 [ Info: 0 records are matched 125.167001 seconds (1.01 G allocations: 53.814 GiB, 11.35% gc time, 0.52% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m18.7s 1.203625 seconds (1.18 M allocations: 68.552 MiB, 4.58% gc time, 85.02% compilation time) 0.951121 seconds (1.09 M allocations: 65.322 MiB, 80.77% compilation time) 1.010597 seconds (1.10 M allocations: 64.358 MiB, 3.42% gc time, 76.77% compilation time) 0.397753 seconds (185.18 k allocations: 10.903 MiB, 99.96% compilation time) 0.010692 seconds (6.15 k allocations: 395.648 KiB, 96.67% compilation time) 0.008909 seconds (2.62 k allocations: 165.945 KiB, 96.58% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 8.9s 0.968102 seconds (965.99 k allocations: 56.871 MiB, 3.76% gc time, 82.02% compilation time) 0.864443 seconds (821.96 k allocations: 50.834 MiB, 79.88% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 5.8s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.100527 seconds (525.06 k allocations: 30.677 MiB, 30.70% compilation time) 0.601521 seconds (634.16 k allocations: 37.629 MiB, 3.17% gc time, 85.09% 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 0.063492 seconds (520.58 k allocations: 32.160 MiB) 0.527178 seconds (584.66 k allocations: 36.248 MiB, 2.80% gc time, 84.94% 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 convert to transpose functions: Test Failed at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 Expression: all(out[1358:var"end", :] .== 0.0) Evaluated: all(Bool[1 1 … 0 0; 1 1 … 0 0; … ; 0 0 … 0 0; 0 0 … 0 0]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] [2] macro expansion @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.559054 seconds (1.56 M allocations: 62.081 MiB, 79.13% gc time, 1.64% compilation time) 0.672260 seconds (1.69 M allocations: 70.184 MiB, 79.37% 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 Fail Total Time convert to transpose functions | 12 1 13 11.2s RNG of the outermost testset: Xoshiro(0x406aecd8346c689b, 0xc402dab6bc124109, 0xf747ae67746962b1, 0xa7d8763c0418aa4a, 0xf7c520a5cb5ec131) ERROR: LoadError: Some tests did not pass: 12 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:72 in expression starting at /home/pkgeval/.julia/packages/VCFTools/IWkMe/test/runtests.jl:17 Testing failed after 1266.3s ERROR: LoadError: Package VCFTools errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1877.27s: package has test failures