Package evaluation of VCFTools on Julia 1.13.0-DEV.791 (d5209bd37d*) started at 2025-07-04T15:08:46.338 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.07s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed CompositionsBase ──────── v0.1.2 Installed Rmath_jll ─────────────── v0.5.1+0 Installed FillArrays ────────────── v1.13.0 Installed CommonSolve ───────────── v0.2.4 Installed DelimitedFiles ────────── v1.9.1 Installed MacroTools ────────────── v0.5.16 Installed DataStructures ────────── v0.18.22 Installed ConstructionBase ──────── v1.6.0 Installed CodecZlib ─────────────── v0.7.8 Installed HypergeometricFunctions ─ v0.3.28 Installed AliasTables ───────────── v1.1.3 Installed OrderedCollections ────── v1.8.1 Installed TranscodingStreams ────── v0.9.13 Installed StatsBase ─────────────── v0.34.5 Installed Compat ────────────────── v4.17.0 Installed DataAPI ───────────────── v1.16.0 Installed StatsAPI ──────────────── v1.7.1 Installed ProgressMeter ─────────── v1.10.4 Installed Combinatorics ─────────── v1.0.3 Installed Statistics ────────────── v1.11.1 Installed VCFTools ──────────────── v0.2.10 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed IrrationalConstants ───── v0.2.4 Installed LogExpFunctions ───────── v0.3.29 Installed BufferedStreams ───────── v1.2.2 Installed QuadGK ────────────────── v2.11.2 Installed Roots ─────────────────── v2.2.8 Installed Rmath ─────────────────── v0.8.0 Installed BioGenerics ───────────── v0.1.5 Installed HypothesisTests ───────── v0.11.5 Installed Distributions ─────────── v0.25.120 Installed StatsFuns ─────────────── v1.5.0 Installed PtrArrays ─────────────── v1.3.0 Installed Reexport ──────────────── v1.2.2 Installed InverseFunctions ──────── v0.1.17 Installed SpecialFunctions ──────── v2.5.1 Installed Missings ──────────────── v1.2.0 Installed Preferences ───────────── v1.4.3 Installed JLLWrappers ───────────── v1.7.0 Installed PDMats ────────────────── v0.11.35 Installed DocStringExtensions ───── v0.9.5 Installed SortingAlgorithms ─────── v1.2.1 Installed Accessors ─────────────── v0.1.42 Installed BGZFStreams ───────────── v0.3.2 Installed VariantCallFormat ─────── v0.5.6 Installed Automa ────────────────── v0.8.4 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 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 v1.7.0 [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 [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 v1.12.0 [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 v1.12.0 [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 6.93s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4480.6 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 341.55s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_66AqgU/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 v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_66AqgU/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 v1.7.0 [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 v1.12.0 [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 v1.12.0 [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 v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+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 3.6s Test Summary: | Pass Total Time openvcf | 4 4 2.3s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.3s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 2.2s ┌ 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: 0:23:51 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 14.308727 seconds (11.13 M allocations: 682.934 MiB, 4.65% gc time, 92.70% compilation time: 20% of which was recompilation) 1.183709 seconds (2.87 M allocations: 195.932 MiB, 5.40% gc time, 6.76% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:21:15 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.947710 seconds (4.42 M allocations: 299.548 MiB, 2.49% gc time, 63.85% compilation time) 0.967679 seconds (2.85 M allocations: 195.342 MiB, 2.23% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.0s 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 1.7s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 1.9s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.9s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 4.8s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:33 Progress: 0%|▏ | ETA: 0:18:21 Progress: 0%|▏ | ETA: 0:17:53 Progress: 0%|▏ | ETA: 0:17:40 Progress: 0%|▎ | ETA: 0:17:27 Progress: 1%|▎ | ETA: 0:17:22 Progress: 1%|▎ | ETA: 0:17:19 Progress: 1%|▍ | ETA: 0:17:19 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100%|█████████████████████████████████████████| Time: 0:01:44 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:55:38 Progress: 21%|████████▌ | ETA: 0:06:25 Progress: 43%|█████████████████▋ | ETA: 0:02:17 Progress: 65%|██████████████████████████▋ | ETA: 0:00:56 Progress: 86%|███████████████████████████████████▍ | ETA: 0:00:17 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 823 records are matched 221.371533 seconds (2.19 G allocations: 143.743 GiB, 6.18% gc time, 0.54% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:37 Progress: 0%|▏ | ETA: 0:18:12 Progress: 0%|▏ | ETA: 0:18:10 Progress: 0%|▏ | ETA: 0:17:40 Progress: 0%|▎ | ETA: 0:17:40 Progress: 1%|▎ | ETA: 0:17:44 Progress: 1%|▎ | ETA: 0:17:50 Progress: 1%|▎ | ETA: 0:17:48 Progress: 1%|▍ | ETA: 0:17:47 Progress: 1%|▍ | ETA: 0:17:46 Progress: 1%|▍ | ETA: 0:17:43 Progress: 1%|▌ | ETA: 0:17:41 Progress: 1%|▌ | ETA: 0:17:38 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target IDs to reference IDs Progress: 0%| | ETA: 19:55:30 Progress: 19%|███████▉ | ETA: 0:07:29 Progress: 38%|███████████████▊ | ETA: 0:02:52 Progress: 60%|████████████████████████▌ | ETA: 0:01:13 Progress: 81%|█████████████████████████████████▏ | ETA: 0:00:26 Progress: 100%|█████████████████████████████████████████| Time: 0:01:50 [ Info: 488 records are matched 229.389736 seconds (2.19 G allocations: 143.726 GiB, 6.15% gc time, 0.36% compilation time) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:03 Progress: 0%|▏ | ETA: 0:19:18 Progress: 0%|▏ | ETA: 0:18:59 Progress: 0%|▏ | ETA: 0:18:29 Progress: 0%|▏ | ETA: 0:18:13 Progress: 1%|▎ | ETA: 0:18:02 Progress: 1%|▎ | ETA: 0:17:51 Progress: 1%|▎ | ETA: 0:17:44 Progress: 1%|▍ | ETA: 0:17:41 Progress: 1%|▍ | ETA: 0:17:38 Progress: 1%|▍ | ETA: 0:17:35 Progress: 1%|▌ | ETA: 0:17:34 Progress: 1%|▌ | ETA: 0:17:32 Progress: 1%|▌ | ETA: 0:17:32 Progress: 1%|▋ | ETA: 0:17:32 Progress: 2%|▋ | ETA: 0:17:31 Progress: 2%|▋ | ETA: 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Progress: 9%|███▋ | ETA: 0:14:08 Progress: 9%|███▋ | ETA: 0:14:08 Progress: 9%|███▊ | ETA: 0:14:08 Progress: 9%|███▊ | ETA: 0:14:08 Progress: 9%|███▊ | ETA: 0:14:08 Progress: 9%|███▉ | ETA: 0:14:08 Progress: 9%|███▉ | ETA: 0:14:08 Progress: 10%|███▉ | ETA: 0:14:08 Progress: 10%|████ | ETA: 0:14:08 Progress: 10%|████ | ETA: 0:14:08 Progress: 10%|████ | ETA: 0:14:07 Progress: 10%|████▏ | ETA: 0:14:07 Progress: 10%|████▏ | ETA: 0:14:07 Progress: 10%|████▏ | ETA: 0:14:07 Progress: 10%|████▎ | ETA: 0:14:07 Progress: 100%|█████████████████████████████████████████| Time: 0:01:37 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 18:59:32 Progress: 29%|████████████ | ETA: 0:04:08 Progress: 58%|███████████████████████▊ | ETA: 0:01:15 Progress: 81%|█████████████████████████████████▏ | ETA: 0:00:25 Progress: 100%|█████████████████████████████████████████| Time: 0:01:45 [ Info: 0 records are matched 214.465307 seconds (2.19 G allocations: 143.726 GiB, 6.52% gc time, 0.37% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 11m12.8s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:10:52 Progress: 19%|███████▋ | ETA: 0:07:57 Progress: 38%|███████████████▌ | ETA: 0:02:59 Progress: 60%|████████████████████████▌ | ETA: 0:01:14 Progress: 82%|█████████████████████████████████▌ | ETA: 0:00:25 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 833 records are matched 123.439528 seconds (1.11 G allocations: 72.817 GiB, 6.07% gc time, 0.47% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:01:29 Progress: 20%|████████ | ETA: 0:07:20 Progress: 40%|████████████████▍ | ETA: 0:02:42 Progress: 62%|█████████████████████████▍ | ETA: 0:01:07 Progress: 84%|██████████████████████████████████▌ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:01:51 [ Info: 493 records are matched 122.510908 seconds (1.11 G allocations: 72.816 GiB, 6.03% gc time, 0.46% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 20:22:06 Progress: 20%|████████▏ | ETA: 0:07:22 Progress: 40%|████████████████▌ | ETA: 0:02:44 Progress: 62%|█████████████████████████▌ | ETA: 0:01:08 Progress: 85%|███████████████████████████████████ | ETA: 0:00:19 Progress: 100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: 0 records are matched 124.064952 seconds (1.11 G allocations: 72.816 GiB, 5.98% gc time, 0.44% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m12.3s 1.173675 seconds (1.35 M allocations: 93.667 MiB, 4.59% gc time, 89.53% compilation time) 1.004076 seconds (1.22 M allocations: 88.656 MiB, 3.81% gc time, 80.07% compilation time) 0.929974 seconds (1.23 M allocations: 87.936 MiB, 2.47% gc time, 83.67% compilation time) 0.421087 seconds (221.15 k allocations: 12.135 MiB, 99.95% compilation time) 0.012492 seconds (6.30 k allocations: 485.242 KiB, 96.41% compilation time) 0.009062 seconds (2.67 k allocations: 248.242 KiB, 96.03% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.5s 0.928222 seconds (994.68 k allocations: 75.905 MiB, 3.67% gc time, 84.03% compilation time) 0.850133 seconds (896.24 k allocations: 72.708 MiB, 2.48% gc time, 83.21% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.2s Test Summary: | Pass Total Time convert_ds | 5 5 1.0s 0.133185 seconds (525.77 k allocations: 50.465 MiB, 14.33% gc time, 27.30% compilation time) 0.668655 seconds (661.51 k allocations: 58.147 MiB, 1.80% gc time, 86.34% 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 0.519084 seconds (520.49 k allocations: 51.920 MiB, 84.37% gc time, 2.16% compilation time: <1% of which was recompilation) 0.557166 seconds (596.83 k allocations: 56.239 MiB, 81.36% 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 … 0 0; 0 0 … 0 0; … ; 0 0 … 0 0; 0 0 … 0 0]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:741 [inlined] [2] macro expansion @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.122075 seconds (1.56 M allocations: 81.839 MiB, 6.98% compilation time) 0.588511 seconds (1.72 M allocations: 90.804 MiB, 4.89% gc time, 75.39% 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 14.8s RNG of the outermost testset: Xoshiro(0x52bdf3c8fd675b00, 0x07acd17b59e8f15c, 0x151fd3bb48207c7a, 0xd15aaa73390b530a, 0x8cde340a0313e2bc) 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 1144.33s ERROR: LoadError: Package VCFTools errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2423 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2278 [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/v1.13/Pkg/src/API.jl:500 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:324 [12] _start() @ Base ./client.jl:557 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1534.65s: package has test failures