Package evaluation to test VCFTools on Julia 1.14.0-DEV.1589 (2d9a3f8a61*) started at 2026-01-21T10:20:48.832 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 10.7s ################################################################################ # 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 v0.1.43 [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 v0.19.3 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [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 v1.5.1 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [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 v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 5.0s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... [ Info: Compiling VCF parser... 15697.3 ms ✓ VariantCallFormat 5818.9 ms ✓ HypothesisTests 6474.7 ms ✓ VCFTools 3 dependencies successfully precompiled in 31 seconds. 113 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 48.89s ################################################################################ # Testing # Testing VCFTools Status `/tmp/jl_oAAYxj/Project.toml` [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [09f84164] HypothesisTests v0.11.6 [92933f4c] ProgressMeter v1.11.0 [276daf66] SpecialFunctions v2.6.1 [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_oAAYxj/Manifest.toml` [7d9f7c33] Accessors v0.1.43 [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 v0.10.15 [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 v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [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 v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [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 v8.18.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 Testing Running tests... Test Summary: | Pass Total Time H-W test | 1 1 3.4s Test Summary: | Pass Total Time openvcf | 4 4 2.0s Test Summary: | Pass Total Time nrecords(vcf) | 1 1 2.2s Test Summary: | Pass Total Time nsamples(vcf) | 1 1 0.0s Test Summary: | Pass Total Time gtstats(record) | 4 4 3.4s ┌ 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: 0:33:46 Progress: 100%|█████████████████████████████████████████| Time: 0:00:04 14.088082 seconds (8.95 M allocations: 542.132 MiB, 5.47% gc time, 92.64% compilation time: 15% of which was recompilation) 0.406074 seconds (2.37 M allocations: 141.102 MiB, 14.43% gc time, 21.78% compilation time: <1% of which was recompilation) Progress: 0%| | ETA: 0:31:54 Progress: 100%|█████████████████████████████████████████| Time: 0:00:03 3.233049 seconds (3.89 M allocations: 236.036 MiB, 1.52% gc time, 87.44% compilation time) 0.426013 seconds (2.37 M allocations: 141.298 MiB, 4.80% gc time) Test Summary: | Pass Total Time gtstats(vcf) | 12 12 21.8s 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 1.8s Test Summary: | Pass Total Time filter_genotype(file) | 4068 4068 2.0s 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 1.6s [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:17:48 Progress: 0%|▏ | ETA: 0:21:36 Progress: 0%|▏ | ETA: 0:19:52 Progress: 0%|▏ | ETA: 0:19:00 Progress: 0%|▎ | ETA: 0:18:25 Progress: 1%|▎ | ETA: 0:19:44 Progress: 1%|▎ | ETA: 0:19:04 Progress: 1%|▍ | ETA: 0:18:43 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100%|█████████████████████████████████████████| Time: 0:01:52 [ Info: Match target IDs to reference IDs Progress: 0%| | ETA: 21:33:09 Progress: 17%|██████▉ | ETA: 0:09:38 Progress: 34%|██████████████ | ETA: 0:03:44 Progress: 52%|█████████████████████▏ | ETA: 0:01:51 Progress: 66%|███████████████████████████▏ | ETA: 0:01:01 Progress: 85%|███████████████████████████████████ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:02:01 [ Info: 823 records are matched 244.251517 seconds (2.01 G allocations: 106.138 GiB, 13.19% gc time, 0.52% compilation time: 6% of which was recompilation) [ Info: Scan IDs in reference panel Progress: 0%| | ETA: 0:19:32 Progress: 0%|▏ | ETA: 0:18:46 Progress: 0%|▏ | ETA: 0:18:41 Progress: 0%|▏ | ETA: 0:18:25 Progress: 0%|▎ | ETA: 0:20:58 Progress: 1%|▎ | ETA: 0:20:57 Progress: 1%|▎ | ETA: 0:20:27 Progress: 1%|▎ | ETA: 0:20:06 Progress: 1%|▍ | ETA: 0:19:46 Progress: 1%|▍ | ETA: 0:19:32 Progress: 1%|▍ | ETA: 0:20:29 Progress: 1%|▌ | 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Progress: 76%|███████████████████████████████▏ | ETA: 0:00:42 Progress: 96%|███████████████████████████████████████▏ | ETA: 0:00:06 Progress: 100%|█████████████████████████████████████████| Time: 0:02:13 [ Info: 0 records are matched 277.220770 seconds (2.01 G allocations: 106.120 GiB, 15.30% gc time, 0.42% compilation time) Test Summary: | Pass Total Time conformgt_by_id | 1649 1649 13m15.3s [ Info: Match target POS to reference POS Progress: 0%| | ETA: 22:43:58 Progress: 6%|██▎ | ETA: 0:34:13 Progress: 22%|████████▉ | ETA: 0:07:26 Progress: 39%|████████████████▏ | ETA: 0:03:12 Progress: 59%|████████████████████████▏ | ETA: 0:01:28 Progress: 78%|████████████████████████████████ | ETA: 0:00:36 Progress: 95%|██████████████████████████████████████▉ | ETA: 0:00:07 Progress: 100%|█████████████████████████████████████████| Time: 0:02:07 [ Info: 833 records are matched 138.098180 seconds (1.02 G allocations: 53.885 GiB, 13.02% gc time, 0.50% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 1 days, 1:02:54 Progress: 19%|███████▊ | ETA: 0:09:40 Progress: 36%|██████████████▉ | ETA: 0:03:59 Progress: 55%|██████████████████████▊ | ETA: 0:01:50 Progress: 75%|██████████████████████████████▋ | ETA: 0:00:47 Progress: 94%|██████████████████████████████████████▋ | ETA: 0:00:09 Progress: 100%|█████████████████████████████████████████| Time: 0:02:19 [ Info: 493 records are matched 150.510128 seconds (1.02 G allocations: 53.884 GiB, 13.90% gc time, 0.46% compilation time) [ Info: Match target POS to reference POS Progress: 0%| | ETA: 23:38:24 Progress: 15%|██████▏ | ETA: 0:12:04 Progress: 32%|█████████████▎ | ETA: 0:04:29 Progress: 51%|████████████████████▊ | ETA: 0:02:06 Progress: 69%|████████████████████████████▏ | ETA: 0:00:59 Progress: 86%|███████████████████████████████████▍ | ETA: 0:00:21 Progress: 100%|█████████████████████████████████████████| Time: 0:02:12 [ Info: 0 records are matched 142.154785 seconds (1.02 G allocations: 53.884 GiB, 13.46% gc time, 0.47% compilation time) Test Summary: | Pass Total Time conformgt_by_pos | 2502 2502 7m13.1s 1.188092 seconds (1.14 M allocations: 65.240 MiB, 83.70% compilation time) 1.014363 seconds (1.05 M allocations: 62.200 MiB, 3.13% gc time, 79.25% compilation time) 0.996057 seconds (1.05 M allocations: 61.236 MiB, 82.38% compilation time) 0.465199 seconds (174.71 k allocations: 10.089 MiB, 99.97% compilation time) 0.013271 seconds (6.05 k allocations: 389.102 KiB, 94.75% compilation time) 0.011410 seconds (2.62 k allocations: 164.711 KiB, 96.90% compilation time) Test Summary: | Pass Total Time convert_gt(vcfile) | 11 11 10.1s 1.112486 seconds (953.20 k allocations: 56.228 MiB, 4.05% gc time, 81.33% compilation time) 0.917474 seconds (812.55 k allocations: 50.397 MiB, 81.55% compilation time) Test Summary: | Pass Total Time convert_ht(vcfile) | 6 6 6.8s Test Summary: | Pass Total Time convert_ds | 5 5 1.1s 0.103637 seconds (525.04 k allocations: 30.674 MiB, 33.04% compilation time) 0.731868 seconds (624.15 k allocations: 36.950 MiB, 3.53% gc time, 84.92% 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 0.090589 seconds (520.58 k allocations: 32.160 MiB, 29.18% gc time) 0.550479 seconds (582.86 k allocations: 36.185 MiB, 85.78% 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/v1.14/Test/src/Test.jl:781 [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:2243 [inlined] [4] top-level scope @ ~/.julia/packages/VCFTools/IWkMe/test/convert_test.jl:73 0.603537 seconds (1.56 M allocations: 62.079 MiB, 80.68% gc time, 1.51% compilation time) 0.607764 seconds (1.68 M allocations: 69.747 MiB, 82.12% 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(0x428c9c6bb8da56f9, 0x198d4d91b1d1591b, 0x91cf7c482f49f9ce, 0x3625c6844168bf49, 0xe34a6027849d7e4f) 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 1334.4s 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:3122 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2987 [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:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1423.38s: package has test failures