Package evaluation to test BGEN on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T16:14:26.392 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.6s ################################################################################ # Installation # Installing BGEN... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [6db4b851] + BGEN v0.2.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [6db4b851] + BGEN v0.2.2 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.5 [2447270c] + GeneticVariantBase v0.1.2 [842dd82b] + InlineStrings v1.4.5 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [43287f4e] + PtrArrays v1.3.0 [fdea26ae] + SIMD v3.7.2 [0aa819cd] + SQLite v1.6.1 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.9 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [76ed43ae] + SQLite_jll v3.48.0+0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.13.0 [fa267f1f] + TOML v1.0.3 [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 v0.8.7+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 Installation completed after 4.65s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:577 Precompilation failed after 13.25s ################################################################################ # Testing # Testing BGEN Status `/tmp/jl_FKLxyl/Project.toml` [6db4b851] BGEN v0.2.2 [2447270c] GeneticVariantBase v0.1.2 [10745b16] Statistics v1.11.1 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_FKLxyl/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [6db4b851] BGEN v0.2.2 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.5 [2447270c] GeneticVariantBase v0.1.2 [842dd82b] InlineStrings v1.4.5 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [43287f4e] PtrArrays v1.3.0 [fdea26ae] SIMD v3.7.2 [0aa819cd] SQLite v1.6.1 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.9 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [76ed43ae] SQLite_jll v3.48.0+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+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 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 Testing Running tests... Test Summary: | Pass Total Time basics | 32 32 10.3s Test Summary: | Pass Total Time getters | 22 22 1.8s Test Summary: | Pass Total Time select_region | 485 485 7.9s Test Summary: | Pass Total Time index | 9 9 1.0s ┌ Warning: Sample names unavailable. Do you have a separate '.sample' file? └ @ BGEN ~/.julia/packages/BGEN/KN7mm/src/sample.jl:7 Test Summary: | Pass Total Time example files | 42601 42601 4.1s ┌ Warning: Sample names unavailable. Do you have a separate '.sample' file? └ @ BGEN ~/.julia/packages/BGEN/KN7mm/src/sample.jl:7 Test Summary: | Pass Total Time minor allele dosage | 1216 1216 3.5s Test Summary: | Pass Total Time utils | 199 199 1.0s Test Summary: | Pass Total Time filter | 1534 1534 4.9s Testing BGEN tests passed Testing completed after 75.01s PkgEval succeeded after 113.08s