Package evaluation to test BED on Julia 1.14.0-DEV.87 (8bcaa34afa*) started at 2025-11-15T09:05:39.833 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.08s ################################################################################ # Installation # Installing BED... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [8e4a8c10] + BED v0.3.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [67c07d97] + Automa v1.1.0 [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 v0.8.5 ⌅ [899a7d2d] + GenomicFeatures v2.1.0 ⌅ [4ffb77ac] + Indexes v0.1.3 [524e6230] + IntervalTrees v1.1.0 [bac558e1] + OrderedCollections v1.8.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [fdea26ae] + SIMD v3.7.2 [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 v1.13.0 [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 [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 To see why use `status --outdated -m` Installation completed after 3.9s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 3854.0 ms ✓ DataStructures 22136.3 ms ✓ Automa 1751.4 ms ✓ GenomicFeatures 1569.1 ms ✓ Indexes 17121.9 ms ✓ BED 5 dependencies successfully precompiled in 47 seconds. 28 already precompiled. Precompilation completed after 59.8s ################################################################################ # Testing # Testing BED Status `/tmp/jl_jm5xpP/Project.toml` [67c07d97] Automa v1.1.0 [8e4a8c10] BED v0.3.1 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 ⌅ [3da002f7] ColorTypes v0.11.5 [31c24e10] Distributions v0.25.122 [e30172f5] Documenter v1.16.0 [53c48c17] FixedPointNumbers v0.8.5 [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_jm5xpP/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [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 v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.16.0 [1a297f60] FillArrays v1.15.0 [53c48c17] FixedPointNumbers v0.8.5 [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 v1.7.1 [682c06a0] JSON v1.3.0 [0e77f7df] LazilyInitializedFields v1.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [d0879d2d] MarkdownAST v0.1.2 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [69de0a69] Parsers v2.8.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [79098fc4] Rmath v0.9.0 [fdea26ae] SIMD v3.7.2 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.8 [4c63d2b9] StatsFuns v1.5.2 [ec057cc2] StructUtils v2.6.0 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [2e619515] Expat_jll v2.7.3+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.51.3+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+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 v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+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 v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+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 [8e850ede] nghttp2_jll v1.68.0+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... 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/EyNRt/src/machine.jl:237 [3] macro expansion @ ~/.julia/packages/Automa/EyNRt/src/codegen.jl:698 [inlined] [4] readrecord!(stream::TranscodingStreams.NoopStream{IOStream}, record::BED.Record, state::Tuple{Int64, Int64}) @ BED ~/.julia/packages/Automa/EyNRt/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 │ @ ~/.julia/packages/BED/CJxEb/src/reader.jl:70 [inlined] ╰──── repeated 2 times [9] (::var"#check_bed_parse#check_bed_parse##0")(filename::String) @ Main ~/.julia/packages/BED/CJxEb/test/runtests.jl:90 [10] eval_test_function(func::Any, args::Any, kwargs::Any, quoted_func::Union{Expr, Symbol}, source::LineNumberNode, negate::Bool) @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:394 [11] top-level scope @ ~/.julia/packages/BED/CJxEb/test/runtests.jl:38 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [13] macro expansion @ ~/.julia/packages/BED/CJxEb/test/runtests.jl:135 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [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/yVko2/src/utilities/utilities.jl:680 [ 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 1m23.9s Record | 42 42 5.2s eachoverlap | 5 5 5.5s Doctests: BED | 1 1 52.8s RNG of the outermost testset: Random.Xoshiro(0x5bb24389520651d7, 0x20e7d78f86c1bf78, 0x2fdf8480f921bf5b, 0x636515b6137bad09, 0x658af8b74c560845) 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 219.77s ERROR: LoadError: Package BED 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:572 [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:548 [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:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 310.39s: package tests unexpectedly errored