Package evaluation to test GFF3 on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-19T14:14:53.300 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.32s ################################################################################ # Installation # Installing GFF3... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [af1dc308] + GFF3 v0.2.3 Updating `~/.julia/environments/v1.12/Manifest.toml` ⌅ [67c07d97] + Automa v0.8.4 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 ⌃ [c2308a5c] + FASTX v2.1.2 [af1dc308] + GFF3 v0.2.3 ⌅ [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 [fdea26ae] + SIMD v3.7.2 [7b38b023] + ScanByte v0.4.0 ⌅ [354b36f9] + StringViews v1.3.7 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [30578b45] + URIParser v0.4.1 [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 [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 [83775a58] + Zlib_jll v1.3.1+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 5.61s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 4945.0 ms ✓ ScanByte 28480.6 ms ✓ FASTX 21369.3 ms ✓ FASTX → BioSequencesExt 24070.1 ms ✓ GFF3 4 dependencies successfully precompiled in 80 seconds. 70 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, 37 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 98.36s ################################################################################ # Testing # Testing GFF3 Status `/tmp/jl_4FN1Mu/Project.toml` ⌅ [67c07d97] Automa v0.8.4 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [e30172f5] Documenter v1.17.0 ⌃ [c2308a5c] FASTX v2.1.2 [3372ea36] FormatSpecimens v1.4.0 [af1dc308] GFF3 v0.2.3 ⌅ [899a7d2d] GenomicFeatures v2.1.0 ⌅ [4ffb77ac] Indexes v0.1.3 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [30578b45] URIParser v0.4.1 [8dfed614] Test v1.11.0 Status `/tmp/jl_4FN1Mu/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 ⌅ [67c07d97] Automa v0.8.4 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [3c28c6f8] BioSymbols v5.2.0 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.18.1 ⌅ [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.17.0 ⌃ [c2308a5c] FASTX v2.1.2 [3372ea36] FormatSpecimens v1.4.0 [af1dc308] GFF3 v0.2.3 ⌅ [899a7d2d] GenomicFeatures v2.1.0 [d7ba0133] Git v1.5.0 [b5f81e59] IOCapture v1.0.0 ⌅ [4ffb77ac] Indexes v0.1.3 [524e6230] IntervalTrees v1.1.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.1 [0e77f7df] LazilyInitializedFields v1.3.0 [d0879d2d] MarkdownAST v0.1.3 ⌅ [bac558e1] OrderedCollections v1.8.2 [69de0a69] Parsers v2.8.6 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [2792f1a3] RegistryInstances v0.1.0 [fdea26ae] SIMD v3.7.2 [7b38b023] ScanByte v0.4.0 ⌅ [354b36f9] StringViews v1.3.7 [ec057cc2] StructUtils v2.8.2 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [30578b45] URIParser v0.4.1 [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 [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 [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 [f489334b] StyledStrings v1.11.0 [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 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.44.0+1 [83775a58] Zlib_jll v1.3.1+2 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling packages... 60560.3 ms ✓ Documenter 1 dependency successfully precompiled in 61 seconds. 53 already precompiled. 18 dependencies precompiled but different versions are currently loaded (Base64, CodecZlib, Dates, InteractiveUtils, JuliaSyntaxHighlighting, Logging, Markdown, PrecompileTools, Preferences, Printf, Serialization, StyledStrings, TOML, Test, TranscodingStreams, UUIDs, Unicode 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. GFF3: Error During Test at /home/pkgeval/.julia/packages/GFF3/ocekA/test/runtests.jl:118 Test threw exception Expression: check_gff3_parse(filepath) GFF3.Record file format error on line 1 ~>"\x1f\x8b\b\x04\0\0\0\0" Stacktrace: [1] error(::Type, ::String, ::Int64, ::String, ::String) @ Base ./error.jl:54 [2] macro expansion @ ~/.julia/packages/GFF3/ocekA/src/reader.jl:381 [inlined] [3] readrecord!(stream::TranscodingStreams.NoopStream{IOStream}, reader::GFF3.Reader{TranscodingStreams.NoopStream{IOStream}}, record::GFF3.Record) @ GFF3 ~/.julia/packages/Automa/Aq8Mq/src/Stream.jl:128 [4] read! @ ~/.julia/packages/GFF3/ocekA/src/reader.jl:113 [inlined] [5] tryread!(reader::GFF3.Reader{TranscodingStreams.NoopStream{IOStream}}, output::GFF3.Record) @ BioGenerics.IO ~/.julia/packages/BioGenerics/53MtO/src/IO.jl:76 [6] iterate(reader::GFF3.Reader{TranscodingStreams.NoopStream{IOStream}}, nextone::GFF3.Record) @ GFF3 ~/.julia/packages/GFF3/ocekA/src/reader.jl:122 [7] iterate @ ~/.julia/packages/GFF3/ocekA/src/reader.jl:122 [inlined] [8] (::var"#check_gff3_parse#check_gff3_parse##0")(filename::String) @ Main ~/.julia/packages/GFF3/ocekA/test/runtests.jl:63 [9] top-level scope @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:18 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1777 [inlined] [11] macro expansion @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:118 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] [13] macro expansion @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:118 [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 GFF3 | 87 1 88 1m31.5s eachoverlap | 4 4 7.2s Doctests: GFF3 | 1 1 1m00.9s RNG of the outermost testset: Random.Xoshiro(0x7dd00922c2201e81, 0xfb22847ac925132c, 0xeca54b5b50992d65, 0x562dec0a3e28a23f, 0x69b383a363a9aab7) ERROR: LoadError: Some tests did not pass: 87 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/GFF3/ocekA/test/runtests.jl:17 Testing failed after 182.41s ERROR: LoadError: Package GFF3 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 312.04s: package tests unexpectedly errored