Package evaluation to test BED on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T13:59:36.493 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 7.91s ################################################################################ # Installation # Installing BED... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [8e4a8c10] + BED v0.3.1 Updating `~/.julia/environments/v1.12/Manifest.toml` [67c07d97] + Automa v1.2.0 [8e4a8c10] + BED v0.3.1 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [944b1d66] + CodecZlib v0.7.8 ⌅ [3da002f7] + ColorTypes v0.11.5 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 ⌅ [53c48c17] + FixedPointNumbers v0.8.6 ⌅ [899a7d2d] + GenomicFeatures v2.1.0 ⌅ [4ffb77ac] + Indexes v0.1.3 [524e6230] + IntervalTrees v1.1.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [10745b16] + Statistics v1.11.1 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [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 [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 v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+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 To see why use `status --outdated -m` Installation completed after 5.7s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 22117.0 ms ✓ Automa 61674.0 ms ✓ Documenter 1908.6 ms ✓ Indexes 14525.7 ms ✓ BED 4 dependencies successfully precompiled in 103 seconds. 95 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 44 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 121.5s ################################################################################ # Testing # Testing BED Status `/tmp/jl_EM1qRe/Project.toml` [67c07d97] Automa v1.2.0 [8e4a8c10] BED v0.3.1 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 ⌅ [3da002f7] ColorTypes v0.11.5 [31c24e10] Distributions v0.25.127 [e30172f5] Documenter v1.17.0 ⌅ [53c48c17] FixedPointNumbers v0.8.6 [3372ea36] FormatSpecimens v1.4.0 ⌅ [899a7d2d] GenomicFeatures v2.1.0 ⌅ [4ffb77ac] Indexes v0.1.3 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_EM1qRe/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.2.0 [8e4a8c10] BED v0.3.1 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [944b1d66] CodecZlib v0.7.8 ⌅ [3da002f7] ColorTypes v0.11.5 [34da2185] Compat v4.18.1 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [31c24e10] Distributions v0.25.127 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.17.0 [1a297f60] FillArrays v1.16.0 ⌅ [53c48c17] FixedPointNumbers v0.8.6 [3372ea36] FormatSpecimens v1.4.0 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [d7ba0133] Git v1.5.0 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v1.0.0 ⌅ [4ffb77ac] Indexes v0.1.3 [524e6230] IntervalTrees v1.1.0 [92d709cd] IrrationalConstants v0.2.6 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.1 [0e77f7df] LazilyInitializedFields v1.3.0 [2ab3a3ac] LogExpFunctions v1.0.1 [d0879d2d] MarkdownAST v0.1.3 [e1d29d7a] Missings v1.2.0 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.6 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [79098fc4] Rmath v0.9.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.8.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.2.0 [ec057cc2] StructUtils v2.8.2 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [2e619515] Expat_jll v2.8.1+0 [020c3dae] Git_LFS_jll v3.7.1+0 [f8c6e375] Git_jll v2.54.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.3.1+0 [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 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [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 v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 2492.1 ms ✓ PDMats → StatsBaseExt 11362.7 ms ✓ Distributions 2 dependencies successfully precompiled in 15 seconds. 47 already precompiled. 16 dependencies precompiled but different versions are currently loaded (Base64, Compat, Compat → CompatLinearAlgebraExt, DataStructures, Dates, InteractiveUtils, JuliaSyntaxHighlighting, Markdown, OrderedCollections, Preferences, Printf, Serialization, Statistics, StyledStrings, TOML and UUIDs). Restart julia to access the new versions. Otherwise, 19 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 3895.1 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 5 seconds. 51 already precompiled. 50 dependencies precompiled but different versions are currently loaded (AliasTables, Base64, Compat, Compat → CompatLinearAlgebraExt, CompilerSupportLibraries_jll, DataAPI, DataStructures, Dates, Distributions, DocStringExtensions, FillArrays, FillArrays → FillArraysPDMatsExt, FillArrays → FillArraysSparseArraysExt, FillArrays → FillArraysStatisticsExt, HypergeometricFunctions, InteractiveUtils, IrrationalConstants, JLLWrappers, JuliaSyntaxHighlighting, LogExpFunctions, Logging, Markdown, Missings, OpenLibm_jll, OpenSpecFun_jll, OrderedCollections, PDMats, PDMats → StatsBaseExt, Preferences, Printf, PtrArrays, QuadGK, Reexport, Rmath, Rmath_jll, Serialization, SortingAlgorithms, SparseArrays, SpecialFunctions, Statistics, Statistics → SparseArraysExt, StatsAPI, StatsBase, StatsFuns, StyledStrings, SuiteSparse, SuiteSparse_jll, TOML, Test and UUIDs). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 58353.4 ms ✓ Documenter 1 dependency successfully precompiled in 59 seconds. 53 already precompiled. 20 dependencies precompiled but different versions are currently loaded (Base64, CodecZlib, CompilerSupportLibraries_jll, Dates, DocStringExtensions, InteractiveUtils, JLLWrappers, JuliaSyntaxHighlighting, Logging, Markdown, PrecompileTools, Preferences, Printf, Serialization, StyledStrings, TOML, Test, TranscodingStreams, UUIDs and Zlib_jll). Restart julia to access the new versions. Otherwise, 21 dependents of these packages may trigger further precompilation to work with the unexpected versions. BED: Error During Test at /home/pkgeval/.julia/packages/BED/CJxEb/test/runtests.jl:135 Test threw exception Expression: check_bed_parse(filepath) Error during FSM execution at buffer position 2. Last 2 byte(s) were: "\x1f\x8b" Observed input: '\x8b' at state 6. Outgoing edges: * '\t'/record_chrom * [ -~] Input is not in any outgoing edge, and machine therefore errored. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] throw_input_error(machine::Automa.Machine, state::Int64, byte::UInt8, memory::Automa.SizedMemory, index::Int64) @ Automa ~/.julia/packages/Automa/fzRJn/src/machine.jl:237 [3] macro expansion @ ~/.julia/packages/Automa/fzRJn/src/codegen.jl:703 [inlined] [4] readrecord!(stream::TranscodingStreams.NoopStream{IOStream}, record::BED.Record, state::Tuple{Int64, Int64}) @ BED ~/.julia/packages/Automa/fzRJn/src/stream.jl:86 [5] read!(rdr::BED.Reader, record::BED.Record) @ BED ~/.julia/packages/BED/CJxEb/src/reader.jl:229 [6] tryread!(reader::BED.Reader, output::BED.Record) @ BioGenerics.IO ~/.julia/packages/BioGenerics/53MtO/src/IO.jl:76 [7] iterate (repeats 2 times) @ ~/.julia/packages/BED/CJxEb/src/reader.jl:70 [inlined] [8] (::var"#check_bed_parse#check_bed_parse##0")(filename::String) @ Main ~/.julia/packages/BED/CJxEb/test/runtests.jl:90 [9] top-level scope @ ~/.julia/packages/BED/CJxEb/test/runtests.jl:38 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1777 [inlined] [11] macro expansion @ ~/.julia/packages/BED/CJxEb/test/runtests.jl:135 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] [13] macro expansion @ ~/.julia/packages/BED/CJxEb/test/runtests.jl:135 [inlined] ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/utilities/utilities.jl:719 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. [ Info: Skipped ExpandTemplates step (doctest only). [ Info: Skipped CrossReferences step (doctest only). [ Info: Skipped CheckDocument step (doctest only). [ Info: Skipped Populate step (doctest only). [ Info: Skipped RenderDocument step (doctest only). Test Summary: | Pass Error Total Time BED | 65 1 66 1m15.1s Record | 42 42 5.5s eachoverlap | 5 5 5.6s Doctests: BED | 1 1 44.1s RNG of the outermost testset: Random.Xoshiro(0xd9f607e805306499, 0x4d391b7f96da82b6, 0x954ed8d36083cc83, 0x6ec161b74d5d1d99, 0xb375428ac9deba79) ERROR: LoadError: Some tests did not pass: 65 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BED/CJxEb/test/runtests.jl:36 Testing failed after 178.8s ERROR: LoadError: Package BED 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{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:2538 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2387 [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/v1.12/Pkg/src/API.jl:552 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:306 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:317 [12] _start() @ Base ./client.jl:550 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 329.77s: package tests unexpectedly errored