Package evaluation to test BigBed on Julia 1.14.0-DEV.1893 (b4aba01002*) started at 2026-03-15T16:25:46.565 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.68s ################################################################################ # Installation # Installing BigBed... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [97aa930e] + BigBed v0.1.0 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [67c07d97] + Automa v0.8.4 [19670fab] + BBI v0.2.1 ⌅ [8e4a8c10] + BED v0.1.1 [28d598bf] + BGZFStreams v0.3.2 [97aa930e] + BigBed v0.1.0 [37cfa864] + BioCore v2.0.5 [47718e42] + BioGenerics v0.1.5 [e1450e63] + BufferedStreams v1.2.2 [944b1d66] + CodecZlib v0.7.8 ⌅ [3da002f7] + ColorTypes v0.9.1 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 ⌅ [53c48c17] + FixedPointNumbers v0.7.1 ⌅ [899a7d2d] + GenomicFeatures v2.1.0 ⌅ [4ffb77ac] + Indexes v0.1.3 [524e6230] + IntervalTrees v1.1.0 [692b3bcd] + JLLWrappers v1.7.1 [2ec943e9] + Libz v1.0.1 [bac558e1] + OrderedCollections v1.8.1 [21216c6a] + Preferences v1.5.2 [69024149] + StringEncodings v0.3.7 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [ddb6d928] + YAML v0.4.16 [94ce4f54] + Libiconv_jll v1.18.0+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 [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 [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 [83775a58] + Zlib_jll v1.3.2+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 To see why use `status --outdated -m` Installation completed after 5.9s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 3116.7 ms ✓ QuadGK 2248.5 ms ✓ GenomicFeatures 2232.0 ms ✓ PDMats → StatsBaseExt 2533.6 ms ✓ BioCore 1885.9 ms ✓ Indexes 11869.0 ms ✓ Distributions 2323.6 ms ✓ BBI 17678.7 ms ✓ BED 4240.0 ms ✓ Distributions → DistributionsTestExt 15742.0 ms ✓ BigBed 10 dependencies successfully precompiled in 65 seconds. 62 already precompiled. 10 dependencies precompiled but different versions are currently loaded (Base64, Dates, JuliaSyntaxHighlighting, Logging, Markdown, Printf, StyledStrings, TOML, UUIDs and Zlib_jll). Restart julia to access the new versions. Otherwise, 35 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 88.64s ################################################################################ # Testing # Testing BigBed Status `/tmp/jl_cfG8Od/Project.toml` ⌅ [67c07d97] Automa v0.8.4 [19670fab] BBI v0.2.1 ⌅ [8e4a8c10] BED v0.1.1 [97aa930e] BigBed v0.1.0 [37cfa864] BioCore v2.0.5 [e1450e63] BufferedStreams v1.2.2 ⌅ [3da002f7] ColorTypes v0.9.1 [31c24e10] Distributions v0.25.123 ⌅ [53c48c17] FixedPointNumbers v0.7.1 [3372ea36] FormatSpecimens v1.4.0 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [2ec943e9] Libz v1.0.1 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_cfG8Od/Manifest.toml` [66dad0bd] AliasTables v1.1.3 ⌅ [67c07d97] Automa v0.8.4 [19670fab] BBI v0.2.1 ⌅ [8e4a8c10] BED v0.1.1 [28d598bf] BGZFStreams v0.3.2 [97aa930e] BigBed v0.1.0 [37cfa864] BioCore v2.0.5 [47718e42] BioGenerics v0.1.5 [e1450e63] BufferedStreams v1.2.2 [944b1d66] CodecZlib v0.7.8 ⌅ [3da002f7] ColorTypes v0.9.1 [34da2185] Compat v4.18.1 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.16.0 ⌅ [53c48c17] FixedPointNumbers v0.7.1 [3372ea36] FormatSpecimens v1.4.0 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [34004b35] HypergeometricFunctions v0.3.28 ⌅ [4ffb77ac] Indexes v0.1.3 [524e6230] IntervalTrees v1.1.0 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.7.1 [2ec943e9] Libz v1.0.1 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [21216c6a] Preferences v1.5.2 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [69024149] StringEncodings v0.3.7 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [ddb6d928] YAML v0.4.16 [94ce4f54] Libiconv_jll v1.18.0+0 [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 [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 [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 v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [8e850b90] libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... empty: Error During Test at /home/pkgeval/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 Got exception outside of a @test EOFError: read end of file Stacktrace: [1] peek @ ./iobuffer.jl:423 [inlined] [2] read @ ./iobuffer.jl:433 [inlined] [3] read(io::IOBuffer, ::Type{BBI.Header}) @ BBI ~/.julia/packages/BBI/9fptT/src/header.jl:26 [4] BigBed.Reader(input::IOBuffer) @ BigBed ~/.julia/packages/BigBed/kcPV4/src/reader.jl:34 [5] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:42 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [9] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:46 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [11] top-level scope @ none:6 [12] eval(m::Module, e::Any) @ Core ./boot.jl:517 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [14] _start() @ Base ./client.jl:585 small: Error During Test at /home/pkgeval/.julia/packages/BigBed/kcPV4/test/runtests.jl:50 Got exception outside of a @test EOFError: read end of file Stacktrace: [1] peek @ ./iobuffer.jl:423 [inlined] [2] read @ ./iobuffer.jl:433 [inlined] [3] read(io::IOBuffer, ::Type{BBI.Header}) @ BBI ~/.julia/packages/BBI/9fptT/src/header.jl:26 [4] BigBed.Reader(input::IOBuffer) @ BigBed ~/.julia/packages/BigBed/kcPV4/src/reader.jl:34 [5] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:51 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [9] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:56 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [11] top-level scope @ none:6 [12] eval(m::Module, e::Any) @ Core ./boot.jl:517 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [14] _start() @ Base ./client.jl:585 large: Error During Test at /home/pkgeval/.julia/packages/BigBed/kcPV4/test/runtests.jl:101 Got exception outside of a @test EOFError: read end of file Stacktrace: [1] peek @ ./iobuffer.jl:423 [inlined] [2] read @ ./iobuffer.jl:433 [inlined] [3] read(io::IOBuffer, ::Type{BBI.Header}) @ BBI ~/.julia/packages/BBI/9fptT/src/header.jl:26 [4] BigBed.Reader(input::IOBuffer) @ BigBed ~/.julia/packages/BigBed/kcPV4/src/reader.jl:34 [5] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:102 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [9] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:118 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [11] top-level scope @ none:6 [12] eval(m::Module, e::Any) @ Core ./boot.jl:517 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [14] _start() @ Base ./client.jl:585 round trip: Error During Test at /home/pkgeval/.julia/packages/BigBed/kcPV4/test/runtests.jl:125 Got exception outside of a @test EOFError: read end of file Stacktrace: [1] peek @ ./iobuffer.jl:423 [inlined] [2] read @ ./iobuffer.jl:433 [inlined] [3] read(io::IOBuffer, ::Type{BBI.Header}) @ BBI ~/.julia/packages/BBI/9fptT/src/header.jl:26 [4] BigBed.Reader(input::IOBuffer) @ BigBed ~/.julia/packages/BigBed/kcPV4/src/reader.jl:34 [5] (::var"#test_round_trip#test_round_trip##0")(filepath::String) @ Main ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:140 [6] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [8] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:126 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [10] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:154 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [12] top-level scope @ none:6 [13] eval(m::Module, e::Any) @ Core ./boot.jl:517 [14] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [15] _start() @ Base ./client.jl:585 overlap: Error During Test at /home/pkgeval/.julia/packages/BigBed/kcPV4/test/runtests.jl:159 Got exception outside of a @test EOFError: read end of file Stacktrace: [1] peek @ ./iobuffer.jl:423 [inlined] [2] read @ ./iobuffer.jl:433 [inlined] [3] read(io::IOBuffer, ::Type{BBI.Header}) @ BBI ~/.julia/packages/BBI/9fptT/src/header.jl:26 [4] BigBed.Reader(input::IOBuffer) @ BigBed ~/.julia/packages/BigBed/kcPV4/src/reader.jl:34 [5] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:160 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [9] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:173 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:324 [11] top-level scope @ none:6 [12] eval(m::Module, e::Any) @ Core ./boot.jl:517 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [14] _start() @ Base ./client.jl:585 Test Summary: | Error Total Time BigBed | 5 5 29.0s empty | 1 1 17.6s small | 1 1 0.4s large | 1 1 0.2s round trip | 1 1 5.9s overlap | 1 1 4.9s RNG of the outermost testset: Random.Xoshiro(0xce02c027990a3638, 0x4fcfec424c7d5afa, 0x436fc6d9c789bdd8, 0x30621a93fb772e47, 0x6150213b4475404f) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 5 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BigBed/kcPV4/test/runtests.jl:40 Testing failed after 48.89s ERROR: LoadError: Package BigBed 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:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [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:586 [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:562 [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:323 [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 176.07s: package tests unexpectedly errored