Package evaluation to test VCFTools on Julia 1.14.0-DEV.2058 (afc71c255e*) started at 2026-04-19T18:58:16.072 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.76s ################################################################################ # 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 v0.1.44 [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 v0.25.124 [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 v1.3.0+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 5.88s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... [ Info: Compiling VCF parser... 16.9 s ✓ VariantCallFormat 6.4 s ✓ VCFTools 2 dependencies successfully precompiled in 36 seconds. 114 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 52.44s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_ltPqhP/Project.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.124 [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_ltPqhP/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 v0.25.124 [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 v2.8.3 [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 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 v1.4.2 [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 2.9s Test Summary: | Pass Total Time openvcf | 4 4 2.2s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.6s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.9s ┌ 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: 0:41:07 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 15.236402 seconds (9.13 M allocations: 552.934 MiB, 1.25% gc time, 95.23% compilation time: 16% of which was recompilation) 0.443420 seconds (2.37 M allocations: 141.180 MiB, 19.04% gc time, 13.52% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:43:42 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 4.413701 seconds (3.95 M allocations: 240.317 MiB, 11.65% gc time, 88.82% compilation time) 0.456484 seconds (2.37 M allocations: 141.313 MiB, 4.43% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 24.1s 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 2.0s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.1s 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 1.1s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:01 Progress: 0%|▏ | ETA: 0:22:36 Progress: 0%|▏ | ETA: 0:20:52 Progress: 0%|▏ | ETA: 0:20:02 Progress: 0%|▎ | ETA: 0:19:33 Progress: 1%|▎ | ETA: 0:20:39 Progress: 1%|▎ | ETA: 0:20:05 Progress: 1%|▎ | ETA: 0:19:37 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100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 19:23:02 Progress: 19%|███████▊ | ETA: 0:07:25 Progress: 38%|███████████████▍ | ETA: 0:02:55 Progress: 59%|████████████████████████▏ | ETA: 0:01:15 Progress: 80%|████████████████████████████████▊ | ETA: 0:00:27 Progress: 98%|████████████████████████████████████████ | ETA: 0:00:03 Progress: 100%|█████████████████████████████████████████| Time: 0:01:49 [ Info: 823 records are matched 232.981223 seconds (2.01 G allocations: 106.069 GiB, 13.53% gc time, 0.60% compilation time: 5% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:25 Progress: 0%|▏ | ETA: 0:21:31 Progress: 0%|▏ | ETA: 0:19:45 Progress: 0%|▏ | ETA: 0:19:09 Progress: 0%|▎ | ETA: 0:18:43 Progress: 1%|▎ | ETA: 0:19:39 Progress: 1%|▎ | ETA: 0:19:19 Progress: 1%|▍ | ETA: 0:18:54 Progress: 1%|▍ | ETA: 0:18:44 Progress: 1%|▍ | ETA: 0:18:34 Progress: 1%|▌ | ETA: 0:19:09 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100%|█████████████████████████████████████████| Time: 0:01:58 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 21:46:59 Progress: 21%|████████▋ | ETA: 0:07:21 Progress: 42%|█████████████████ | ETA: 0:02:46 Progress: 61%|████████████████████████▉ | ETA: 0:01:18 Progress: 83%|██████████████████████████████████▎ | ETA: 0:00:24 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 0 records are matched 250.005288 seconds (2.01 G allocations: 106.050 GiB, 13.15% gc time, 0.39% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m17.3s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:05:35 Progress: 20%|████████▏ | ETA: 0:07:39 Progress: 39%|████████████████▏ | ETA: 0:02:57 Progress: 60%|████████████████████████▋ | ETA: 0:01:17 Progress: 83%|██████████████████████████████████▎ | ETA: 0:00:23 Progress: 100%|█████████████████████████████████████████| Time: 0:01:58 [ Info: 833 records are matched 128.194697 seconds (1.01 G allocations: 53.815 GiB, 11.38% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:00:04 Progress: 10%|████▏ | ETA: 0:16:59 Progress: 28%|███████████▎ | ETA: 0:04:59 Progress: 50%|████████████████████▌ | ETA: 0:01:55 Progress: 72%|█████████████████████████████▌ | ETA: 0:00:45 Progress: 93%|██████████████████████████████████████ | ETA: 0:00:09 Progress: 100%|█████████████████████████████████████████| Time: 0:01:57 [ Info: 493 records are matched 127.708413 seconds (1.01 G allocations: 53.814 GiB, 11.44% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:36:12 Progress: 19%|███████▋ | ETA: 0:08:25 Progress: 37%|███████████████▏ | ETA: 0:03:20 Progress: 54%|██████████████████████▏ | ETA: 0:01:41 Progress: 74%|██████████████████████████████▍ | ETA: 0:00:42 Progress: 96%|███████████████████████████████████████▍ | ETA: 0:00:05 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 0 records are matched 131.343387 seconds (1.01 G allocations: 53.814 GiB, 12.37% gc time, 0.46% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m29.6s 1.221984 seconds (1.18 M allocations: 68.556 MiB, 85.07% compilation time) 1.144854 seconds (1.09 M allocations: 65.311 MiB, 81.96% compilation time) 1.156561 seconds (1.10 M allocations: 64.360 MiB, 82.13% compilation time) 0.483933 seconds (185.19 k allocations: 10.920 MiB, 99.95% compilation time) 0.014330 seconds (6.15 k allocations: 395.648 KiB, 96.67% compilation time) 0.010298 seconds (2.62 k allocations: 165.945 KiB, 96.31% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 10.1s 1.050879 seconds (965.97 k allocations: 56.869 MiB, 82.82% compilation time) 1.028149 seconds (821.97 k allocations: 50.836 MiB, 5.26% gc time, 82.90% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.6s Test Summary: | Pass Total Time convert_ds | 5 5 1.2s 0.101330 seconds (525.06 k allocations: 30.677 MiB, 32.04% compilation time) 0.663861 seconds (634.17 k allocations: 37.673 MiB, 4.09% gc time, 85.79% 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 0.058761 seconds (520.58 k allocations: 32.160 MiB) 0.632135 seconds (584.66 k allocations: 36.243 MiB, 3.05% gc time, 85.90% 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; … ; 1 1 … 0 0; 1 1 … 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 0.111789 seconds (1.56 M allocations: 62.080 MiB, 8.87% compilation time) 1.349367 seconds (1.69 M allocations: 70.193 MiB, 44.32% gc time, 47.47% 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 13.2s RNG of the outermost testset: Xoshiro(0x5dfb2f12ba798028, 0x5edd7bddb8e2c094, 0x99f46ffe7e4a9e24, 0x17895fcd54a99b2d, 0x211b7141ad3a16d3) 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 1240.03s 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 1351.93s: package has test failures