Package evaluation to test SequenceVariation on Julia 1.14.0-DEV.2291 (26145852c4*) started at 2026-06-04T13:42:22.740 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.9s ################################################################################ # Installation # Installing SequenceVariation... Resolving package versions... Installed BioGenerics ──────── v0.1.5 Installed BioAlignments ────── v3.1.0 Installed SequenceVariation ── v0.2.2 Installed BioSymbols ───────── v5.2.0 Installed Twiddle ──────────── v1.1.2 Installed BioSequences ─────── v3.5.1 Installed Preferences ──────── v1.5.2 Installed PrecompileTools ──── v1.3.4 Installed TranscodingStreams ─ v0.11.3 Installed IntervalTrees ────── v1.1.0 Updating `~/.julia/environments/v1.14/Project.toml` [eef6e190] + SequenceVariation v0.2.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [00701ae9] + BioAlignments v3.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.1 [3c28c6f8] + BioSymbols v5.2.0 [524e6230] + IntervalTrees v1.1.0 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [eef6e190] + SequenceVariation v0.2.2 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0 [4536629a] + OpenBLAS_jll v0.3.33+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 4.87s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5.1 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 0.8 s ✓ Twiddle 0.9 s ✓ IntervalTrees 1.0 s ✓ TranscodingStreams 0.9 s ✓ Compat 1.4 s ✓ Preferences 0.7 s ✓ BioGenerics 0.6 s ✓ Compat → CompatLinearAlgebraExt 1.9 s ✓ PrecompileTools 7.5 s ✓ Aqua 3.5 s ✓ BioSymbols 12.7 s ✓ BioSequences 4.1 s ✓ BioAlignments 1.7 s ✓ SequenceVariation 13 dependencies successfully precompiled in 38 seconds. 30 already precompiled. Precompilation completed after 70.34s ################################################################################ # Testing # Testing SequenceVariation Status `/tmp/jl_eSdTLg/Project.toml` ⌅ [4c88cf16] Aqua v0.6.7 [00701ae9] BioAlignments v3.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [3c28c6f8] BioSymbols v5.2.0 [eef6e190] SequenceVariation v0.2.2 [8dfed614] Test v1.11.0 Status `/tmp/jl_eSdTLg/Manifest.toml` ⌅ [4c88cf16] Aqua v0.6.7 [00701ae9] BioAlignments v3.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [3c28c6f8] BioSymbols v5.2.0 [34da2185] Compat v4.18.1 [524e6230] IntervalTrees v1.1.0 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [eef6e190] SequenceVariation v0.2.2 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [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 v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [f489334b] StyledStrings v1.13.0 [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 v1.5.2+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.4+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time EditSorting | 2 2 0.1s Test Summary: | Pass Total Time HaplotypeValidation | 11 11 2.7s Test Summary: | Pass Total Time HaplotypeRoundtrip | 8 8 0.4s Test Summary: | Pass Total Time HaplotypeReconstruction | 1 1 0.7s Test Summary: | Pass Total Time VariationSorting | 1 1 0.0s Test Summary: | Pass Total Time HaplotypeTranslation | 1 1 0.6s Test Summary: | Pass Total Time VariationPosition | 1 1 0.4s Test Summary: | Pass Total Time VariationParsing | 3 3 0.0s Test Summary: | Pass Total Time VariationRetrieval | 1 1 0.0s Test Summary: | Pass Total Time VariationTranslation | 10 10 0.1s Test Summary: | Pass Total Time VariationBases | 14 14 0.4s Test Summary: | Pass Total Time SoftclipHaplotype | 4 4 0.0s ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.var"#undefined_exports##0#undefined_exports##1"{Vector{Symbol}}, x::Module) at exports.jl:5 └ @ Aqua ~/.julia/packages/Aqua/zpdNP/src/exports.jl:5 ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.Piracy.var"#3#4"{Bool, IdSet{Any}, Vector{Method}}, x::Module) at exports.jl:5 └ @ Aqua ~/.julia/packages/Aqua/zpdNP/src/exports.jl:5 Possible type-piracy detected: [1] Deletion(len::UInt64) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Deletion.jl:10 [2] Deletion(x::Integer) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Deletion.jl:15 [3] Haplotype(aln::PairwiseAlignment{T, T}) where T<:(LongSequence{<:Union{AminoAcidAlphabet, NucleicAcidAlphabet}}) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/Haplotype.jl:114 [4] SequenceVariation.Inapplicable() @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/SequenceVariation.jl:45 [5] Insertion(s::BioSequence) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Insertion.jl:15 [6] Substitution(x::T) where T<:BioSymbol @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Substitution.jl:8 [7] SequenceVariation.Unsafe() @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/SequenceVariation.jl:44 [8] Variation(ref::S, edit::AbstractString) where S<:BioSequence @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/Variation.jl:41 Aqua: Test Failed at /home/pkgeval/.julia/packages/Aqua/zpdNP/src/piracy.jl:206 Expression: isempty(v) Evaluated: isempty(Method[Deletion(len::UInt64) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Deletion.jl:10, Deletion(x::Integer) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Deletion.jl:15, Haplotype(aln::PairwiseAlignment{T, T}) where T<:(LongSequence{<:Union{AminoAcidAlphabet, NucleicAcidAlphabet}}) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/Haplotype.jl:114, SequenceVariation.Inapplicable() @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/SequenceVariation.jl:45, Insertion(s::BioSequence) @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Insertion.jl:15, Substitution(x::T) where T<:BioSymbol @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/edits/Substitution.jl:8, SequenceVariation.Unsafe() @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/SequenceVariation.jl:44, Variation(ref::S, edit::AbstractString) where S<:BioSequence @ SequenceVariation ~/.julia/packages/SequenceVariation/y7qGk/src/Variation.jl:41]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] [2] test_piracy(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/zpdNP/src/piracy.jl:206 [3] test_piracy(m::Module) @ Aqua ~/.julia/packages/Aqua/zpdNP/src/piracy.jl:191 [4] top-level scope @ ~/.julia/packages/SequenceVariation/y7qGk/test/runtests.jl:278 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [6] macro expansion @ ~/.julia/packages/SequenceVariation/y7qGk/test/runtests.jl:283 [inlined] Test Summary: | Pass Fail Total Time Aqua | 7 1 8 40.6s Base.PkgId(Base.UUID("eef6e190-9969-4f06-a38f-35a110a8fdc8"), "SequenceVariation") | 1 1 0.0s Base.PkgId(Base.UUID("eef6e190-9969-4f06-a38f-35a110a8fdc8"), "SequenceVariation") | 1 1 0.0s Base.PkgId(Base.UUID("eef6e190-9969-4f06-a38f-35a110a8fdc8"), "SequenceVariation") | 1 1 0.0s /home/pkgeval/.julia/packages/SequenceVariation/y7qGk/Project.toml | 1 1 0.0s /home/pkgeval/.julia/packages/SequenceVariation/y7qGk/docs/Project.toml | 1 1 0.0s RNG of the outermost testset: Random.Xoshiro(0x1f0f1736bfcaf1c5, 0x3073c45c4ef6e06c, 0x81ed0da3f0191a7e, 0x6c5a425a786e32ab, 0x308378f8a8307a2c) ERROR: LoadError: Some tests did not pass: 7 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SequenceVariation/y7qGk/test/runtests.jl:277 Testing failed after 69.3s ERROR: LoadError: Package SequenceVariation 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:3247 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:326 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 179.01s: package has test failures