Package evaluation of BigBed on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T11:30:08.803 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.51s ################################################################################ # Installation # Installing BigBed... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [97aa930e] + BigBed v0.1.0 Updating `~/.julia/environments/v1.11/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 v4.16.0 [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 v1.7.0 [2ec943e9] + Libz v1.0.1 [bac558e1] + OrderedCollections v1.8.0 [21216c6a] + Preferences v1.4.3 [69024149] + StringEncodings v0.3.7 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [ddb6d928] + YAML v0.4.13 [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 [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 v0.7.0 [9e88b42a] + Serialization v1.11.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [83775a58] + Zlib_jll v1.2.13+1 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 To see why use `status --outdated -m` Installation completed after 2.65s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 53.06s ################################################################################ # Testing # Testing BigBed Status `/tmp/jl_0LmIYd/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 v0.25.118 ⌅ [53c48c17] FixedPointNumbers v0.7.1 [3372ea36] FormatSpecimens v1.3.1 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [2ec943e9] Libz v1.0.1 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_0LmIYd/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 v4.16.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [1a297f60] FillArrays v1.13.0 ⌅ [53c48c17] FixedPointNumbers v0.7.1 [3372ea36] FormatSpecimens v1.3.1 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [34004b35] HypergeometricFunctions v0.3.28 ⌅ [4ffb77ac] Indexes v0.1.3 [524e6230] IntervalTrees v1.1.0 [92d709cd] IrrationalConstants v0.2.4 [692b3bcd] JLLWrappers v1.7.0 [2ec943e9] Libz v1.0.1 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [21216c6a] Preferences v1.4.3 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [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 [4c63d2b9] StatsFuns v1.4.0 [69024149] StringEncodings v0.3.7 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [ddb6d928] YAML v0.4.13 [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 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra 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 v0.7.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.11.0 [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 v1.1.1+0 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [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. 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:201 [inlined] [2] read @ ./iobuffer.jl:211 [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] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:46 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:42 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [9] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [10] include(fname::String) @ Main ./sysimg.jl:38 [11] top-level scope @ none:6 [12] eval @ ./boot.jl:430 [inlined] [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [14] _start() @ Base ./client.jl:531 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:201 [inlined] [2] read @ ./iobuffer.jl:211 [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] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:56 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:51 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [9] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [10] include(fname::String) @ Main ./sysimg.jl:38 [11] top-level scope @ none:6 [12] eval @ ./boot.jl:430 [inlined] [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [14] _start() @ Base ./client.jl:531 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:201 [inlined] [2] read @ ./iobuffer.jl:211 [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] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:118 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:102 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [9] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [10] include(fname::String) @ Main ./sysimg.jl:38 [11] top-level scope @ none:6 [12] eval @ ./boot.jl:430 [inlined] [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [14] _start() @ Base ./client.jl:531 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:201 [inlined] [2] read @ ./iobuffer.jl:211 [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#4")(filepath::String) @ Main ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:140 [6] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:154 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [8] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:126 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [10] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [11] include(fname::String) @ Main ./sysimg.jl:38 [12] top-level scope @ none:6 [13] eval @ ./boot.jl:430 [inlined] [14] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [15] _start() @ Base ./client.jl:531 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:201 [inlined] [2] read @ ./iobuffer.jl:211 [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] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:173 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [7] macro expansion @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:160 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [9] top-level scope @ ~/.julia/packages/BigBed/kcPV4/test/runtests.jl:41 [10] include(fname::String) @ Main ./sysimg.jl:38 [11] top-level scope @ none:6 [12] eval @ ./boot.jl:430 [inlined] [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [14] _start() @ Base ./client.jl:531 Test Summary: | Error Total Time BigBed | 5 5 35.3s empty | 1 1 16.7s small | 1 1 0.5s large | 1 1 0.4s round trip | 1 1 10.8s overlap | 1 1 6.8s 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 48.45s ERROR: LoadError: Package BigBed errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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/v1.11/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/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/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 126.14s: package tests unexpectedly errored