Package evaluation to test VCFTools on Julia 1.14.0-DEV.2407 (ce8c59448a*) started at 2026-06-18T19:34:48.092 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.4s ################################################################################ # 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 v1.2.0 [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 v0.2.7 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.5 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.126 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.8 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.8.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [90014a1f] + PDMats v0.11.37 [aea7be01] + PrecompileTools v1.3.4 [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 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.1.0 [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 v1.14.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [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 v1.5.3+0 [4536629a] + OpenBLAS_jll v0.3.33+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 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 4.71s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... [ Info: Compiling VCF parser... 14.8 s ✓ VariantCallFormat 6.4 s ✓ VCFTools 2 dependencies successfully precompiled in 23 seconds. 113 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 50.38s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_CZQyNQ/Project.toml` [336ed68f] CSV v0.10.16 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.126 [09f84164] HypothesisTests v0.11.8 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.14.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_CZQyNQ/Manifest.toml` [7d9f7c33] Accessors v0.1.44 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.2.0 [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 v0.2.7 [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 v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.126 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.8 [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 v1.8.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v1.0.1 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.6 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [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 [91c51154] SentinelArrays v1.4.10 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.8.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.1.0 [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 v1.2.0 [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 v1.14.0 [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 v1.13.0 [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 v1.5.3+0 [deac9b47] LibCURL_jll v8.20.0+1 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.7+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 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 2.2s Test Summary: | Pass Total Time openvcf | 4 4 1.9s 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 3.4s ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 ┌ 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: 0:43:08 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 14.916593 seconds (7.05 M allocations: 444.679 MiB, 2.07% gc time, 94.87% compilation time: 6% of which was recompilation) 0.494476 seconds (2.37 M allocations: 141.118 MiB, 8.54% gc time, 11.77% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:43:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 4.357320 seconds (3.20 M allocations: 196.382 MiB, 1.48% gc time, 87.47% compilation time) 0.694946 seconds (2.37 M allocations: 141.510 MiB, 23.60% gc time, 1.43% compilation time: <1% of which was recompilation) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 23.8s 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 2.4s 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 1.0s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:20:14 Progress: 0%|▏ | ETA: 0:22:29 Progress: 0%|▏ | ETA: 0:21:47 Progress: 0%|▏ | ETA: 0:21:16 Progress: 0%|▏ | ETA: 0:20:54 Progress: 1%|▎ | ETA: 0:21:00 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0:17:34 Progress: 10%|████ | ETA: 0:17:33 Progress: 10%|████ | ETA: 0:17:32 Progress: 10%|████ | ETA: 0:17:31 Progress: 10%|████ | ETA: 0:17:29 Progress: 10%|████▏ | ETA: 0:17:28 Progress: 10%|████▏ | ETA: 0:17:27 Progress: 10%|████▏ | ETA: 0:17:27 Progress: 10%|████▎ | ETA: 0:17:25 Progress: 10%|████▎ | ETA: 0:17:24 Progress: 100%|█████████████████████████████████████████| Time: 0:02:00 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 22:02:19 Progress: 19%|███████▊ | ETA: 0:08:30 Progress: 37%|███████████████▎ | ETA: 0:03:22 Progress: 58%|███████████████████████▊ | ETA: 0:01:28 Progress: 78%|████████████████████████████████▏ | ETA: 0:00:34 Progress: 99%|████████████████████████████████████████▋| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: 0 records are matched 253.606948 seconds (2.01 G allocations: 106.049 GiB, 7.43% gc time, 0.40% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 12m56.2s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 21:53:08 Progress: 16%|██████▍ | ETA: 0:10:37 Progress: 34%|██████████████ | ETA: 0:03:47 Progress: 53%|█████████████████████▋ | ETA: 0:01:47 Progress: 70%|████████████████████████████▉ | ETA: 0:00:51 Progress: 91%|█████████████████████████████████████▎ | ETA: 0:00:12 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: 833 records are matched 132.446644 seconds (1.01 G allocations: 53.814 GiB, 7.09% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:00:56 Progress: 19%|███████▋ | ETA: 0:08:32 Progress: 37%|███████████████▏ | ETA: 0:03:23 Progress: 55%|██████████████████████▊ | ETA: 0:01:37 Progress: 74%|██████████████████████████████▌ | ETA: 0:00:42 Progress: 94%|██████████████████████████████████████▍ | ETA: 0:00:08 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: 493 records are matched 133.043295 seconds (1.01 G allocations: 53.814 GiB, 7.17% gc time, 0.49% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:04:07 Progress: 18%|███████▌ | ETA: 0:08:44 Progress: 38%|███████████████▌ | ETA: 0:03:17 Progress: 57%|███████████████████████▎ | ETA: 0:01:32 Progress: 76%|███████████████████████████████ | ETA: 0:00:39 Progress: 95%|███████████████████████████████████████ | ETA: 0:00:06 Progress: 100%|█████████████████████████████████████████| Time: 0:02:02 [ Info: 0 records are matched 133.144911 seconds (1.01 G allocations: 53.814 GiB, 6.92% gc time, 0.52% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 6m41.0s 1.223948 seconds (1.10 M allocations: 65.826 MiB, 1.95% gc time, 76.59% compilation time) 1.057117 seconds (1.02 M allocations: 62.882 MiB, 1.72% gc time, 73.04% compilation time) 1.040733 seconds (1.02 M allocations: 61.932 MiB, 75.47% compilation time) 0.443998 seconds (163.58 k allocations: 10.199 MiB, 99.95% compilation time) 0.011494 seconds (5.42 k allocations: 364.711 KiB, 94.71% compilation time) 0.011846 seconds (2.60 k allocations: 164.852 KiB, 95.31% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 9.4s 1.080934 seconds (911.48 k allocations: 55.257 MiB, 2.48% gc time, 77.15% compilation time) 1.004187 seconds (779.77 k allocations: 49.423 MiB, 1.93% gc time, 72.86% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.5s Test Summary: | Pass Total Time convert_ds | 5 5 1.2s 0.164789 seconds (524.56 k allocations: 30.666 MiB, 17.44% compilation time) 0.673541 seconds (617.20 k allocations: 37.125 MiB, 1.79% gc time, 78.36% 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 0.158342 seconds (520.58 k allocations: 32.160 MiB, 11.81% gc time) 0.671768 seconds (575.73 k allocations: 35.908 MiB, 73.52% 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 … 1 1; 1 1 … 1 1; … ; 1 1 … 1 1; 1 1 … 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 0.231960 seconds (1.56 M allocations: 62.080 MiB, 15.26% gc time, 3.63% compilation time) 0.762021 seconds (1.67 M allocations: 69.524 MiB, 3.27% gc time, 73.99% 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 12.1s RNG of the outermost testset: Xoshiro(0x0132746a2f037a00, 0xc6c0a9a09f4bb508, 0x08d40e72acf98f99, 0xafe4134ea755ece4, 0x50d540b0011fe151) 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 1288.13s 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:3247 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1376.74s: package has test failures