Package evaluation of VCFTools on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T09:36:58.024 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.2s ################################################################################ # Installation # Installing VCFTools... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [a620830f] + VCFTools v0.2.10 Updating `~/.julia/environments/v1.10/Manifest.toml` [7d9f7c33] + Accessors v0.1.41 [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 v1.0.2 [38540f10] + CommonSolve v0.2.4 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.20 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.27 [09f84164] + HypothesisTests v0.11.3 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.2 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.5 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.3.2 ⌅ [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 [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [b77e0a4c] + InteractiveUtils [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.1+4 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+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 7.76s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 23.68s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_besywh/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.117 [09f84164] HypothesisTests v0.11.3 [92933f4c] ProgressMeter v1.10.2 [276daf66] SpecialFunctions v2.5.0 [2913bbd2] StatsBase v0.34.4 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.6 [ade2ca70] Dates [f43a241f] Downloads v1.6.0 [37e2e46d] LinearAlgebra [9a3f8284] Random [8dfed614] Test Status `/tmp/jl_besywh/Manifest.toml` [7d9f7c33] Accessors v0.1.41 [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 v1.0.2 [38540f10] CommonSolve v0.2.4 [34da2185] Compat v4.16.0 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.5.8 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.117 [ffbed154] DocStringExtensions v0.9.3 [48062228] FilePathsBase v0.9.23 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.27 [09f84164] HypothesisTests v0.11.3 [842dd82b] InlineStrings v1.4.3 [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 v0.5.15 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.2 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.5 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.3.2 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 ⌅ [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 v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [de0858da] Printf [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.1+4 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 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 2.9s Test Summary: | Pass Total Time openvcf | 4 4 1.3s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 1.7s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.1s Test Summary: | Pass Total Time gtstats(record) | 4 4 1.6s ┌ 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: 0:15:22 Progress: 100%|█████████████████████████████████████████| Time: 0:00:02 6.478557 seconds (2.81 M allocations: 255.126 MiB, 1.77% gc time, 89.47% compilation time) 0.529213 seconds (825.26 k allocations: 120.025 MiB, 2.53% gc time, 15.01% compilation time) Progress: 0%| | ETA: 0:16:49 Progress: 100%|█████████████████████████████████████████| Time: 0:00:01 1.992951 seconds (1.38 M allocations: 155.367 MiB, 1.45% gc time, 74.77% compilation time) 0.511285 seconds (824.52 k allocations: 119.525 MiB, 1.92% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 11.2s 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 1.1s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 1.3s Test Summary: | Pass Total Time flip_gt_allele | 4 4 0.6s Test Summary: | Pass Total Time match_gt_allele | 4 4 0.1s Test Summary: | Pass Total Time binomial_proportion_test | 2 2 1.8s [ Info: Scan IDs in reference panel Progress: 0%|▏ | ETA: 0:08:42 Progress: 0%|▏ | ETA: 0:08:32 Progress: 1%|▎ | ETA: 0:08:28 Progress: 1%|▍ | ETA: 0:08:25 Progress: 1%|▍ | ETA: 0:08:16 Progress: 1%|▌ | ETA: 0:08:12 Progress: 1%|▋ | ETA: 0:08:13 Progress: 2%|▋ | ETA: 0:08:13 Progress: 2%|▊ | ETA: 0:08:12 Progress: 2%|▉ | ETA: 0:08:10 Progress: 2%|▉ | ETA: 0:08:08 Progress: 2%|█ | ETA: 0:08:09 Progress: 3%|█▏ | ETA: 0:08:07 Progress: 3%|█▏ | ETA: 0:08:04 Progress: 3%|█▎ | ETA: 0:08:02 Progress: 3%|█▍ | ETA: 0:08:02 Progress: 3%|█▍ | ETA: 0:08:02 Progress: 4%|█▌ | ETA: 0:08:01 Progress: 4%|█▋ | ETA: 0:08:00 Progress: 4%|█▋ | ETA: 0:08:00 Progress: 4%|█▊ | ETA: 0:07:59 Progress: 4%|█▉ | ETA: 0:07:59 Progress: 5%|█▉ | ETA: 0:07:58 Progress: 5%|██ | ETA: 0:07:57 Progress: 5%|██▏ | ETA: 0:07:56 Progress: 5%|██▏ | ETA: 0:07:55 Progress: 5%|██▎ | ETA: 0:07:55 Progress: 6%|██▍ | ETA: 0:07:54 Progress: 6%|██▍ | ETA: 0:07:52 Progress: 6%|██▌ | ETA: 0:07:51 Progress: 6%|██▋ | ETA: 0:07:50 Progress: 6%|██▋ | ETA: 0:07:49 Progress: 7%|██▊ | ETA: 0:07:48 Progress: 7%|██▉ | ETA: 0:07:47 Progress: 7%|██▉ | ETA: 0:07:46 Progress: 7%|███ | ETA: 0:07:45 Progress: 7%|███▏ | ETA: 0:07:44 Progress: 8%|███▏ | ETA: 0:07:42 Progress: 8%|███▎ | ETA: 0:07:41 Progress: 8%|███▍ | ETA: 0:07:40 Progress: 8%|███▍ | ETA: 0:07:39 Progress: 9%|███▌ | ETA: 0:07:38 Progress: 9%|███▋ | ETA: 0:07:37 Progress: 9%|███▋ | ETA: 0:07:35 Progress: 9%|███▊ | ETA: 0:07:34 Progress: 9%|███▉ | ETA: 0:07:33 Progress: 10%|███▉ | ETA: 0:07:31 Progress: 10%|████ | ETA: 0:07:30 Progress: 10%|████▏ | ETA: 0:07:29 Progress: 10%|████▏ | ETA: 0:07:28 Progress: 100%|█████████████████████████████████████████| Time: 0:00:51 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 9:35:47 Progress: 22%|█████████▎ | ETA: 0:03:00 Progress: 47%|███████████████████▍ | ETA: 0:01:00 Progress: 72%|█████████████████████████████▍ | ETA: 0:00:21 Progress: 98%|████████████████████████████████████████▎| ETA: 0:00:01 Progress: 100%|█████████████████████████████████████████| Time: 0:00:55 [ Info: 823 records are matched 117.278273 seconds (678.89 M allocations: 70.715 GiB, 5.47% gc time, 0.07% compilation time) [ Info: Scan IDs in reference panel Progress: 0%|▏ | ETA: 0:08:21 Progress: 0%|▏ | ETA: 0:08:11 Progress: 1%|▎ | ETA: 0:08:06 Progress: 1%|▍ | ETA: 0:08:07 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Info: 0 records are matched 117.528008 seconds (678.83 M allocations: 70.719 GiB, 5.28% gc time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 5m57.7s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 9:22:16 Progress: 23%|█████████▋ | ETA: 0:02:46 Progress: 49%|████████████████████▏ | ETA: 0:00:54 Progress: 75%|██████████████████████████████▊ | ETA: 0:00:18 Progress: 100%|█████████████████████████████████████████| Time: 0:00:53 [ Info: 833 records are matched 63.857539 seconds (348.98 M allocations: 36.350 GiB, 4.38% gc time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 9:17:19 Progress: 24%|██████████ | ETA: 0:02:37 Progress: 50%|████████████████████▌ | ETA: 0:00:52 Progress: 75%|██████████████████████████████▉ | ETA: 0:00:17 Progress: 100%|█████████████████████████████████████████| Time: 0:00:53 [ Info: 493 records are matched 63.366393 seconds (348.98 M allocations: 36.353 GiB, 4.28% gc time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 9:20:39 Progress: 26%|██████████▋ | ETA: 0:02:25 Progress: 52%|█████████████████████▍ | ETA: 0:00:48 Progress: 80%|████████████████████████████████▉ | ETA: 0:00:13 Progress: 100%|█████████████████████████████████████████| Time: 0:00:53 [ Info: 0 records are matched 63.489229 seconds (348.98 M allocations: 36.352 GiB, 4.51% gc time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 3m11.8s 0.888386 seconds (982.09 k allocations: 84.510 MiB, 4.35% gc time, 78.37% compilation time) 0.639183 seconds (849.70 k allocations: 77.248 MiB, 1.64% gc time, 75.81% compilation time) 0.639102 seconds (855.36 k allocations: 76.625 MiB, 3.06% gc time, 76.02% compilation time) 0.407554 seconds (144.83 k allocations: 9.716 MiB, 99.95% compilation time) 0.011657 seconds (4.77 k allocations: 441.742 KiB, 95.94% compilation time) 0.009838 seconds (2.39 k allocations: 254.281 KiB, 95.76% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 7.8s 0.452480 seconds (563.41 k allocations: 57.191 MiB, 19.14% gc time, 49.79% compilation time) 0.468289 seconds (521.97 k allocations: 56.305 MiB, 60.28% gc time, 2.35% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 4.1s Test Summary: | Pass Total Time convert_ds | 5 5 0.8s 0.148848 seconds (521.50 k allocations: 54.254 MiB, 18.98% gc time, 9.42% compilation time) 0.113534 seconds (519.89 k allocations: 54.142 MiB, 6.57% gc time, 8.32% 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 0.093827 seconds (519.85 k allocations: 55.869 MiB, 2.61% gc time) 0.106205 seconds (519.87 k allocations: 55.870 MiB, 2.52% gc time, 9.81% 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:end, :] .== 0.0) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:672 [inlined] [2] macro expansion @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:119 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.451338 seconds (1.56 M allocations: 107.492 MiB, 54.96% gc time) 0.199551 seconds (1.56 M allocations: 107.494 MiB, 2.91% gc time, 5.02% 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 5.2s 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 737.29s ERROR: LoadError: Package VCFTools errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 785.52s: package has test failures