Package evaluation to test GFF3 on Julia 1.11.8 (29b3528cce*) started at 2026-01-20T04:12:34.055 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.11` Set-up completed after 8.76s ################################################################################ # Installation # Installing GFF3... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [af1dc308] + GFF3 v0.2.3 Updating `~/.julia/environments/v1.11/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 v1.8.1 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.1 [fdea26ae] + SIMD v3.7.2 [7b38b023] + ScanByte v0.4.0 [354b36f9] + StringViews v1.3.6 ⌅ [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 [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 ⌃ 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 To see why use `status --outdated -m` Installation completed after 5.22s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 1849.7 ms ✓ ScanByte 23451.8 ms ✓ FASTX 2578.7 ms ✓ FASTX → BioSequencesExt 19619.2 ms ✓ GFF3 4 dependencies successfully precompiled in 49 seconds. 69 already precompiled. Precompilation completed after 63.26s ################################################################################ # Testing # Testing GFF3 Status `/tmp/jl_Bg02nA/Project.toml` ⌅ [67c07d97] Automa v0.8.4 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [e30172f5] Documenter v1.16.1 ⌃ [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_Bg02nA/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 v1.16.1 ⌃ [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 v1.7.1 [682c06a0] JSON v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [d0879d2d] MarkdownAST v0.1.2 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [2792f1a3] RegistryInstances v0.1.0 [fdea26ae] SIMD v3.7.2 [7b38b023] ScanByte v0.4.0 [354b36f9] StringViews v1.3.6 [ec057cc2] StructUtils v2.6.2 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [7200193e] Twiddle v1.1.2 [30578b45] URIParser v0.4.1 [2e619515] Expat_jll v2.7.3+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.52.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+0 [458c3c95] OpenSSL_jll v3.5.4+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [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 v1.2.0 [44cfe95a] Pkg v1.11.0 [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 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [efcefdf7] PCRE2_jll v10.42.0+1 [83775a58] Zlib_jll v1.2.13+1 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+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. Testing Running tests... Precompiling Documenter... 59491.1 ms ✓ Documenter 1 dependency successfully precompiled in 60 seconds. 52 already precompiled. 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:44 [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#4")(filename::String) @ Main ~/.julia/packages/GFF3/ocekA/test/runtests.jl:63 [9] macro expansion @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:118 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:677 [inlined] [11] macro expansion @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:118 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] top-level scope @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:18 ┌ 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/xvqbW/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 GFF3 | 87 1 88 1m15.0s eachoverlap | 4 4 7.1s Doctests: GFF3 | 1 1 48.2s 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 154.35s ERROR: LoadError: Package GFF3 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:2128 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [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:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 245.93s: package tests unexpectedly errored