Package evaluation of BGEN on Julia 1.12.0-DEV.1805 (a080deafdd*) started at 2025-03-24T16:25:28.402 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.4s ################################################################################ # Installation # Installing BGEN... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [6db4b851] + BGEN v0.2.1 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [6db4b851] + BGEN v0.2.1 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.6 [34da2185] + Compat v4.16.0 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.3 [2447270c] + GeneticVariantBase v0.1.2 [842dd82b] + InlineStrings v1.4.3 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [69de0a69] + Parsers v2.8.1 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [43287f4e] + PtrArrays v1.3.0 [fdea26ae] + SIMD v3.7.1 [0aa819cd] + SQLite v1.6.1 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [ea10d353] + WeakRefStrings v1.4.2 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [76ed43ae] + SQLite_jll v3.48.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [dc6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.2.0+0 [e37daf67] + LibGit2_jll v1.8.0+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+1 [4536629a] + OpenBLAS_jll v0.3.28+3 [05823500] + OpenLibm_jll v0.8.1+3 [bea87d4a] + SuiteSparse_jll v7.8.0+1 [83775a58] + Zlib_jll v1.3.1+1 [8e850b90] + libblastrampoline_jll v5.11.2+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 1.88s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 28.84s ################################################################################ # Testing # Testing BGEN Status `/tmp/jl_Nocxek/Project.toml` [6db4b851] BGEN v0.2.1 [2447270c] GeneticVariantBase v0.1.2 [10745b16] Statistics v1.11.1 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Nocxek/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [6db4b851] BGEN v0.2.1 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.6 [34da2185] Compat v4.16.0 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.3 [2447270c] GeneticVariantBase v0.1.2 [842dd82b] InlineStrings v1.4.3 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [69de0a69] Parsers v2.8.1 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.3.0 [fdea26ae] SIMD v3.7.1 [0aa819cd] SQLite v1.6.1 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [ea10d353] WeakRefStrings v1.4.2 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [76ed43ae] SQLite_jll v3.48.0+0 [3161d3a3] Zstd_jll v1.5.7+1 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [dc6e5ff7] JuliaSyntaxHighlighting v1.12.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.2.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.2.0+0 [e37daf67] LibGit2_jll v1.8.0+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+1 [4536629a] OpenBLAS_jll v0.3.28+3 [05823500] OpenLibm_jll v0.8.1+3 [bea87d4a] SuiteSparse_jll v7.8.0+1 [83775a58] Zlib_jll v1.3.1+1 [8e850b90] libblastrampoline_jll v5.11.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 23098.6 ms ✓ BGEN 1 dependency successfully precompiled in 25 seconds. 61 already precompiled. preamble: Error During Test at /home/pkgeval/.julia/packages/BGEN/VXCjF/test/test_basics.jl:47 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::BGEN.BgenVariant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/VXCjF/src/genotypes.jl:72 [4] decompress(io::IOStream, v::BGEN.BgenVariant, h::BGEN.Header) @ BGEN ~/.julia/packages/BGEN/VXCjF/src/genotypes.jl:42 [5] top-level scope @ ~/.julia/packages/BGEN/VXCjF/test/test_basics.jl:2 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined] [7] macro expansion @ ~/.julia/packages/BGEN/VXCjF/test/test_basics.jl:48 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1724 [inlined] [9] macro expansion @ ~/.julia/packages/BGEN/VXCjF/test/test_basics.jl:49 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:301 [11] top-level scope @ ~/.julia/packages/BGEN/VXCjF/test/runtests.jl:12 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:301 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core ./boot.jl:485 [15] exec_options(opts::Base.JLOptions) @ Base ./client.jl:295 [16] _start() @ Base ./client.jl:558 Test Summary: | Pass Error Total Time basics | 24 1 25 12.1s header | 7 7 1.9s samples_separate | 2 2 2.0s bgen | 15 15 3.0s preamble | 1 1 3.7s ERROR: LoadError: Some tests did not pass: 24 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BGEN/VXCjF/test/test_basics.jl:1 in expression starting at /home/pkgeval/.julia/packages/BGEN/VXCjF/test/runtests.jl:12 Testing failed after 62.29s ERROR: LoadError: Package BGEN errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:68 [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/v1.12/Pkg/src/Operations.jl:2359 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2214 [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::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:159 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:146 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:300 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:329 [12] _start() @ Base ./client.jl:558 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 118.53s: package tests unexpectedly errored