Package evaluation to test GFF3 on Julia 1.14.0-DEV.87 (8bcaa34afa*) started at 2025-11-15T09:12:44 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.57s ################################################################################ # Installation # Installing GFF3... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [af1dc308] + GFF3 v0.2.3 Updating `~/.julia/environments/v1.14/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 v1.3.3 [21216c6a] + Preferences v1.5.0 [fdea26ae] + SIMD v3.7.2 [7b38b023] + ScanByte v0.4.0 [354b36f9] + StringViews v1.3.5 ⌅ [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 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 [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 To see why use `status --outdated -m` Installation completed after 4.24s ################################################################################ # Precompilation # Precompiling PkgEval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... 2346.6 ms ✓ Automa 4924.6 ms ✓ DataStructures 5428.9 ms ✓ ScanByte 2934.1 ms ✓ GenomicFeatures 25963.4 ms ✓ FASTX 1768.0 ms ✓ Indexes 19538.2 ms ✓ GFF3 7 dependencies successfully precompiled in 63 seconds. 27 already precompiled. Precompilation completed after 72.04s ################################################################################ # Testing # Testing GFF3 Status `/tmp/jl_wW36tu/Project.toml` ⌅ [67c07d97] Automa v0.8.4 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.0 [e30172f5] Documenter v1.16.0 ⌃ [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_wW36tu/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 v3.5.0 [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 v1.16.0 ⌃ [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 v1.7.1 [682c06a0] JSON v1.3.0 [0e77f7df] LazilyInitializedFields v1.3.0 [d0879d2d] MarkdownAST v0.1.2 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [2792f1a3] RegistryInstances v0.1.0 [fdea26ae] SIMD v3.7.2 [7b38b023] ScanByte v0.4.0 [354b36f9] StringViews v1.3.5 [ec057cc2] StructUtils v2.6.0 ⌅ [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 v2.51.3+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+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 [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 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850ede] nghttp2_jll v1.68.0+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... 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] 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 [10] top-level scope @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:18 [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [12] macro expansion @ ~/.julia/packages/GFF3/ocekA/test/runtests.jl:118 [inlined] [13] 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 GFF3 | 87 1 88 1m29.7s eachoverlap | 4 4 6.8s Doctests: GFF3 | 1 1 1m00.7s RNG of the outermost testset: Random.Xoshiro(0x3361a1f442437071, 0xe2949f8b30745052, 0xe3e1ad86d94aabe5, 0x8c9613d4c668cf0e, 0x26a26f097ef36642) 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 145.87s ERROR: LoadError: Package GFF3 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 318.11s: package tests unexpectedly errored