Package evaluation to test VCFTools on Julia 1.14.0-DEV.2028 (45a2de3f7a*) started at 2026-04-12T21:53:11.090 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.68s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed Rmath_jll ─────────────── v0.5.1+0 Installed CompositionsBase ──────── v0.1.2 Installed CommonSolve ───────────── v0.2.6 Installed MacroTools ────────────── v0.5.16 Installed DelimitedFiles ────────── v1.9.1 Installed DataStructures ────────── v0.19.4 Installed FillArrays ────────────── v1.16.0 Installed VCFTools ──────────────── v0.2.10 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed CodecZlib ─────────────── v0.7.8 Installed OrderedCollections ────── v1.8.1 Installed HypergeometricFunctions ─ v0.3.28 Installed StatsBase ─────────────── v0.34.10 Installed TranscodingStreams ────── v0.11.3 Installed HypothesisTests ───────── v0.11.6 Installed Combinatorics ─────────── v1.1.0 Installed DataAPI ───────────────── v1.16.0 Installed StatsAPI ──────────────── v1.8.0 Installed SIMD ──────────────────── v3.7.2 Installed Statistics ────────────── v1.11.1 Installed PrecompileTools ───────── v1.3.3 Installed ProgressMeter ─────────── v1.11.0 Installed IrrationalConstants ───── v0.2.6 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed QuadGK ────────────────── v2.11.3 Installed LogExpFunctions ───────── v0.3.29 Installed Rmath ─────────────────── v0.9.0 Installed BufferedStreams ───────── v1.2.2 Installed StatsFuns ─────────────── v1.5.2 Installed BioGenerics ───────────── v0.1.5 Installed Roots ─────────────────── v2.3.0 Installed Distributions ─────────── v0.25.123 Installed Reexport ──────────────── v1.2.2 Installed InverseFunctions ──────── v0.1.17 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.1 Installed PtrArrays ─────────────── v1.4.0 Installed SortingAlgorithms ─────── v1.2.2 Installed SpecialFunctions ──────── v2.7.2 Installed Preferences ───────────── v1.5.2 Installed PDMats ────────────────── v0.11.37 Installed BGZFStreams ───────────── v0.3.2 Installed Automa ────────────────── v1.1.0 Installed VariantCallFormat ─────── v0.5.9 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.44 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 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 v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [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 v1.5.2 [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 v2.3.0 [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 v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.30+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 10.44s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5133.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 4732.7 ms ✓ MacroTools 1878.1 ms ✓ InlineStrings 947.0 ms ✓ Reexport 1363.7 ms ✓ Statistics 1113.8 ms ✓ DataAPI 1483.1 ms ✓ ConstructionBase 2474.6 ms ✓ IrrationalConstants 970.4 ms ✓ DataValueInterfaces 1079.1 ms ✓ StatsAPI 1655.3 ms ✓ OrderedCollections 1074.2 ms ✓ InvertedIndices 1173.1 ms ✓ InverseFunctions 1034.1 ms ✓ CompositionsBase 1335.3 ms ✓ DocStringExtensions 2465.6 ms ✓ Combinatorics 1217.7 ms ✓ WorkerUtilities 2497.7 ms ✓ FillArrays 1227.1 ms ✓ BufferedStreams 998.1 ms ✓ PtrArrays 934.9 ms ✓ CommonSolve 1484.3 ms ✓ TranscodingStreams 928.2 ms ✓ IteratorInterfaceExtensions 1019.5 ms ✓ LaTeXStrings 2206.0 ms ✓ Crayons 1160.6 ms ✓ DelimitedFiles 2283.8 ms ✓ PDMats 2062.4 ms ✓ ProgressMeter 2757.1 ms ✓ SentinelArrays 1367.6 ms ✓ Compat 1648.5 ms ✓ Preferences 1674.5 ms ✓ Statistics → SparseArraysExt 1137.0 ms ✓ Missings 1179.7 ms ✓ PooledArrays 945.5 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 4329.6 ms ✓ DataStructures 1825.6 ms ✓ InverseFunctions → InverseFunctionsTestExt 1383.8 ms ✓ InverseFunctions → InverseFunctionsDatesExt 956.3 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1553.7 ms ✓ LogExpFunctions 1874.7 ms ✓ FillArrays → FillArraysSparseArraysExt 1226.1 ms ✓ FillArrays → FillArraysStatisticsExt 1231.5 ms ✓ AliasTables 1124.7 ms ✓ BioGenerics 1267.6 ms ✓ CodecZlib 1120.5 ms ✓ TableTraits 1792.0 ms ✓ FillArrays → FillArraysPDMatsExt 1016.5 ms ✓ Compat → CompatLinearAlgebraExt 1733.5 ms ✓ JLLWrappers 1402.5 ms ✓ PrecompileTools 1349.0 ms ✓ SortingAlgorithms 2727.0 ms ✓ QuadGK 6069.1 ms ✓ Accessors 969.8 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1215.3 ms ✓ BGZFStreams 2195.3 ms ✓ Tables 2807.9 ms ✓ FilePathsBase 2473.0 ms ✓ Rmath_jll 2494.0 ms ✓ OpenSpecFun_jll 4374.1 ms ✓ StringManipulation 16291.5 ms ✓ SIMD 18772.0 ms ✓ Parsers 5299.2 ms ✓ StatsBase 2877.7 ms ✓ Accessors → LinearAlgebraExt 2331.9 ms ✓ Accessors → TestExt 3419.7 ms ✓ FilePathsBase → FilePathsBaseTestExt 1496.9 ms ✓ FilePathsBase → FilePathsBaseMmapExt 2017.4 ms ✓ Rmath 6110.3 ms ✓ SpecialFunctions 46935.0 ms ✓ PrettyTables 21043.4 ms ✓ Automa 1553.7 ms ✓ InlineStrings → ParsersExt 1823.9 ms ✓ PDMats → StatsBaseExt 8623.6 ms ✓ Roots 2967.6 ms ✓ HypergeometricFunctions 94744.5 ms ✓ DataFrames [ Info: Compiling VCF parser... 17775.1 ms ✓ VariantCallFormat 3320.0 ms ✓ WeakRefStrings 3791.0 ms ✓ StatsFuns 29810.4 ms ✓ CSV 1504.9 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 10228.7 ms ✓ Distributions 4382.5 ms ✓ Distributions → DistributionsTestExt 5011.2 ms ✓ HypothesisTests 5438.4 ms ✓ VCFTools 84 dependencies successfully precompiled in 422 seconds. 32 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 458.56s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_qETt34/Project.toml` [336ed68f] CSV v0.10.16 [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 v2.7.2 [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_qETt34/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 v1.8.1 [864edb3b] DataStructures v0.19.4 [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 v1.16.0 [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 v1.5.2 [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 v2.3.0 [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 v1.4.2 [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 v8.19.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.30+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 v1.68.1+0 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.2s Test Summary: | Pass Total Time openvcf | 4 4 2.3s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 4.4s ┌ Warning: `Progress(n::Integer, dt::Real, desc::AbstractString = "Progress: ", barlen = nothing, color::Symbol = :green, output::IO = stderr; offset::Integer = 0)` is deprecated, use `Progress(n; dt = dt, desc = desc, barlen = barlen, color = color, output = output, offset = offset)` instead. │ caller = ip:0x0 └ @ Core :-1 Progress: 0%| | ETA: 0:34:38 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 15.490501 seconds (9.12 M allocations: 552.842 MiB, 1.22% gc time, 95.71% compilation time: 17% of which was recompilation) 1.066674 seconds (2.37 M allocations: 141.048 MiB, 63.19% gc time, 5.70% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:37:09 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.832014 seconds (3.95 M allocations: 240.234 MiB, 0.79% gc time, 87.11% compilation time) 0.495147 seconds (2.37 M allocations: 141.423 MiB, 2.28% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 24.3s 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 2.1s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.4s 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 1.6s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:51 Progress: 0%|▏ | ETA: 0:20:15 Progress: 0%|▏ | ETA: 0:25:34 Progress: 0%|▏ | ETA: 0:24:40 Progress: 0%|▏ | ETA: 0:23:58 Progress: 0%|▎ | ETA: 0:23:36 Progress: 1%|▎ | ETA: 0:23:19 Progress: 1%|▎ | ETA: 0:23:07 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Progress: 10%|████▎ | ETA: 0:20:06 Progress: 10%|████▎ | ETA: 0:20:04 Progress: 100%|█████████████████████████████████████████| Time: 0:02:18 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 1 days, 2:25:11 Progress: 17%|██████▉ | ETA: 0:11:36 Progress: 34%|██████████████ | ETA: 0:04:34 Progress: 51%|█████████████████████ | ETA: 0:02:17 Progress: 68%|███████████████████████████▊ | ETA: 0:01:10 Progress: 87%|███████████████████████████████████▉ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:02:26 [ Info: 0 records are matched 296.042108 seconds (2.01 G allocations: 106.050 GiB, 13.48% gc time, 0.32% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 14m57.7s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 1:59:05 Progress: 16%|██████▍ | ETA: 0:12:35 Progress: 33%|█████████████▋ | ETA: 0:04:43 Progress: 50%|████████████████████▍ | ETA: 0:02:24 Progress: 66%|███████████████████████████▏ | ETA: 0:01:13 Progress: 85%|██████████████████████████████████▉ | ETA: 0:00:25 Progress: 100%|█████████████████████████████████████████| Time: 0:02:25 [ Info: 833 records are matched 155.463521 seconds (1.01 G allocations: 53.815 GiB, 13.00% gc time, 0.40% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 1:46:32 Progress: 15%|██████▎ | ETA: 0:12:58 Progress: 31%|████████████▉ | ETA: 0:05:05 Progress: 49%|████████████████████▎ | ETA: 0:02:24 Progress: 68%|███████████████████████████▊ | ETA: 0:01:08 Progress: 86%|███████████████████████████████████▏ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:02:24 [ Info: 493 records are matched 154.632070 seconds (1.01 G allocations: 53.814 GiB, 12.59% gc time, 0.45% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 0:28:59 Progress: 14%|█████▋ | ETA: 0:13:45 Progress: 39%|████████████████ | ETA: 0:03:27 Progress: 70%|████████████████████████████▋ | ETA: 0:00:58 Progress: 93%|██████████████████████████████████████▎ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:02:15 [ Info: 0 records are matched 145.016778 seconds (1.01 G allocations: 53.814 GiB, 12.70% gc time, 0.44% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 7m37.9s 0.914612 seconds (1.18 M allocations: 68.545 MiB, 2.68% gc time, 81.77% compilation time) 0.709343 seconds (1.09 M allocations: 65.307 MiB, 81.06% compilation time) 0.726092 seconds (1.10 M allocations: 64.355 MiB, 3.24% gc time, 78.66% compilation time) 0.300834 seconds (185.18 k allocations: 10.919 MiB, 99.96% compilation time) 0.008483 seconds (6.15 k allocations: 395.648 KiB, 96.74% compilation time) 0.008541 seconds (2.62 k allocations: 165.945 KiB, 95.84% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 7.2s 0.924995 seconds (965.96 k allocations: 56.867 MiB, 80.53% compilation time) 0.890022 seconds (821.97 k allocations: 50.852 MiB, 4.07% gc time, 74.79% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.1s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.103345 seconds (525.06 k allocations: 30.677 MiB, 30.53% compilation time) 0.623635 seconds (634.18 k allocations: 37.675 MiB, 4.10% gc time, 83.90% 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 0.089020 seconds (520.58 k allocations: 32.160 MiB, 25.23% gc time) 0.583222 seconds (584.66 k allocations: 36.243 MiB, 88.08% 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[0 0 … 1 1; 0 0 … 1 1; … ; 0 0 … 1 1; 0 0 … 1 1]) 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 0.118992 seconds (1.56 M allocations: 62.081 MiB, 6.99% compilation time) 0.766537 seconds (1.69 M allocations: 70.189 MiB, 75.59% 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 11.9s RNG of the outermost testset: Xoshiro(0xade1e0b6a2b8131e, 0xace00a20a9d79ae9, 0x860266ea9fa52a6a, 0x6b60e8bd84c16d7a, 0x42345edc5fc2b641) 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 1463.49s 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:3160 [3] test @ /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] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [14] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1977.52s: package has test failures