Package evaluation of VCFTools on Julia 1.13.0-DEV.880 (5ebc5b463e*) started at 2025-07-22T18:52:05.218 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 11.53s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Installed CompositionsBase ──────── v0.1.2 Installed Rmath_jll ─────────────── v0.5.1+0 Installed FillArrays ────────────── v1.13.0 Installed DelimitedFiles ────────── v1.9.1 Installed CommonSolve ───────────── v0.2.4 Installed MacroTools ────────────── v0.5.16 Installed DataStructures ────────── v0.18.22 Installed VCFTools ──────────────── v0.2.10 Installed CodecZlib ─────────────── v0.7.8 Installed ConstructionBase ──────── v1.6.0 Installed AliasTables ───────────── v1.1.3 Installed HypergeometricFunctions ─ v0.3.28 Installed OrderedCollections ────── v1.8.1 Installed StatsBase ─────────────── v0.34.5 Installed TranscodingStreams ────── v0.9.13 Installed Compat ────────────────── v4.17.0 Installed DataAPI ───────────────── v1.16.0 Installed Combinatorics ─────────── v1.0.3 Installed IrrationalConstants ───── v0.2.4 Installed ProgressMeter ─────────── v1.10.4 Installed Statistics ────────────── v1.11.1 Installed StatsAPI ──────────────── v1.7.1 Installed QuadGK ────────────────── v2.11.2 Installed OpenSpecFun_jll ───────── v0.5.6+0 Installed Rmath ─────────────────── v0.8.0 Installed LogExpFunctions ───────── v0.3.29 Installed BufferedStreams ───────── v1.2.2 Installed HypothesisTests ───────── v0.11.5 Installed StatsFuns ─────────────── v1.5.0 Installed BioGenerics ───────────── v0.1.5 Installed Roots ─────────────────── v2.2.8 Installed Distributions ─────────── v0.25.120 Installed PtrArrays ─────────────── v1.3.0 Installed InverseFunctions ──────── v0.1.17 Installed Reexport ──────────────── v1.2.2 Installed Missings ──────────────── v1.2.0 Installed JLLWrappers ───────────── v1.7.0 Installed SpecialFunctions ──────── v2.5.1 Installed Preferences ───────────── v1.4.3 Installed SortingAlgorithms ─────── v1.2.1 Installed PDMats ────────────────── v0.11.35 Installed DocStringExtensions ───── v0.9.5 Installed Accessors ─────────────── v0.1.42 Installed Automa ────────────────── v0.8.4 Installed VariantCallFormat ─────── v0.5.6 Installed BGZFStreams ───────────── v0.3.2 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 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 7.89s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4998.8 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 365.87s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_QwG8B8/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_QwG8B8/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 v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+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 3.8s Test Summary: | Pass Total Time openvcf | 4 4 2.6s 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 2.3s ┌ 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: 0:19:56 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 13.060482 seconds (10.61 M allocations: 665.597 MiB, 4.36% gc time, 92.38% compilation time: 21% of which was recompilation) 0.438454 seconds (2.86 M allocations: 195.788 MiB, 10.34% gc time, 18.81% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:22:04 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 2.350360 seconds (4.37 M allocations: 297.823 MiB, 3.06% gc time, 83.18% compilation time) 0.380824 seconds (2.85 M allocations: 195.535 MiB, 6.73% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 19.9s 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 1.8s 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 5.9s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:18:17 Progress: 0%|▏ | ETA: 0:17:19 Progress: 0%|▏ | ETA: 0:16:53 Progress: 0%|▏ | ETA: 0:16:52 Progress: 0%|▎ | ETA: 0:16:53 Progress: 1%|▎ | ETA: 0:16:55 Progress: 1%|▎ | ETA: 0:16:54 Progress: 1%|▍ | ETA: 0:16:52 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0:01:19 [ Info: 0 records are matched 191.159776 seconds (2.19 G allocations: 143.726 GiB, 7.74% gc time, 0.50% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 10m52.2s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 14:12:55 Progress: 28%|███████████▍ | ETA: 0:03:20 Progress: 58%|███████████████████████▋ | ETA: 0:00:57 Progress: 89%|████████████████████████████████████▍ | ETA: 0:00:10 Progress: 100%|█████████████████████████████████████████| Time: 0:01:18 [ Info: 833 records are matched 86.999971 seconds (1.11 G allocations: 72.817 GiB, 7.93% gc time, 0.59% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 13:57:51 Progress: 30%|████████████▏ | ETA: 0:02:59 Progress: 61%|█████████████████████████ | ETA: 0:00:49 Progress: 93%|██████████████████████████████████████▎ | ETA: 0:00:06 Progress: 100%|█████████████████████████████████████████| Time: 0:01:17 [ Info: 493 records are matched 85.477870 seconds (1.11 G allocations: 72.816 GiB, 7.62% gc time, 0.48% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 13:35:48 Progress: 29%|████████████ | ETA: 0:02:56 Progress: 62%|█████████████████████████▍ | ETA: 0:00:46 Progress: 96%|███████████████████████████████████████▎ | ETA: 0:00:03 Progress: 100%|█████████████████████████████████████████| Time: 0:01:15 [ Info: 0 records are matched 83.655648 seconds (1.11 G allocations: 72.816 GiB, 7.46% gc time, 0.49% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 4m17.7s 0.774449 seconds (1.28 M allocations: 91.367 MiB, 3.19% gc time, 88.93% compilation time) 0.665348 seconds (1.16 M allocations: 86.628 MiB, 3.97% gc time, 81.18% compilation time) 0.638467 seconds (1.16 M allocations: 85.883 MiB, 3.02% gc time, 83.26% compilation time) 0.292454 seconds (203.61 k allocations: 11.564 MiB, 99.95% compilation time) 0.008587 seconds (6.18 k allocations: 483.492 KiB, 96.70% compilation time) 0.007748 seconds (2.65 k allocations: 247.555 KiB, 96.36% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 6.6s 0.646641 seconds (952.92 k allocations: 74.547 MiB, 4.73% gc time, 82.37% compilation time) 0.553697 seconds (861.52 k allocations: 71.597 MiB, 3.41% gc time, 82.23% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 4.3s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.097944 seconds (525.31 k allocations: 50.449 MiB, 27.13% compilation time) 0.503777 seconds (647.53 k allocations: 57.716 MiB, 83.44% 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 0.072434 seconds (520.43 k allocations: 51.916 MiB, 37.66% gc time) 0.410998 seconds (589.76 k allocations: 56.017 MiB, 5.71% gc time, 75.66% 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/v1.13/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:1858 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.111691 seconds (1.56 M allocations: 81.839 MiB, 23.75% gc time, 6.95% compilation time) 0.447474 seconds (1.70 M allocations: 90.369 MiB, 4.24% gc time, 77.82% 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 8.8s RNG of the outermost testset: Xoshiro(0xbad12b359b1f2305, 0xf0318857e28eefbd, 0xc2d73981a64f66cf, 0xa3f541a720136064, 0xd54eaf5762e09703) 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 999.94s 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:2661 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2510 [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:537 [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:168 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [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:320 [12] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1410.41s: package has test failures