Package evaluation to test BioSequenceMappings on Julia 1.14.0-DEV.3055 (7e75a8061a*) started at 2026-08-27T17:47:49.403 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.35s ################################################################################ # Installation # Installing BioSequenceMappings... Resolving package versions... Installed Adapt ──────────────── v4.7.0 Installed MacroTools ─────────── v0.5.16 Installed BioSequenceMappings ── v0.1.7 Installed StringViews ────────── v1.3.7 Installed HashArrayMappedTries ─ v0.2.0 Installed Compat ─────────────── v4.18.1 Installed TranscodingStreams ─── v0.11.3 Installed Statistics ─────────── v1.11.1 Installed PrecompileTools ────── v1.3.4 Installed GPUArraysCore ──────── v0.2.0 Installed ProgressMeter ──────── v1.11.0 Installed ArgCheck ───────────── v2.5.0 Installed StaticArraysCore ───── v1.4.4 Installed Atomix ─────────────── v1.1.3 Installed StaticArrays ───────── v1.9.19 Installed NNlib ──────────────── v0.9.44 Installed ChainRulesCore ─────── v1.26.1 Installed BioGenerics ────────── v0.1.5 Installed UnsafeAtomics ──────── v0.3.2 Installed ScopedValues ───────── v1.6.2 Installed Requires ───────────── v1.3.1 Installed FASTX ──────────────── v2.1.7 Installed Automa ─────────────── v1.2.0 Installed KernelAbstractions ─── v0.9.42 Installed Preferences ────────── v1.5.2 Installed BFloat16s ──────────── v0.6.1 Installed OneHotArrays ───────── v0.2.11 Updating `~/.julia/environments/v1.14/Project.toml` [a84bc454] + BioSequenceMappings v0.1.7 Updating `~/.julia/environments/v1.14/Manifest.toml` [79e6a3ab] + Adapt v4.7.0 [dce04be8] + ArgCheck v2.5.0 [a9b6321e] + Atomix v1.1.3 [67c07d97] + Automa v1.2.0 [ab4f0b2a] + BFloat16s v0.6.1 [47718e42] + BioGenerics v0.1.5 [a84bc454] + BioSequenceMappings v0.1.7 [d360d2e6] + ChainRulesCore v1.26.1 [34da2185] + Compat v4.18.1 [c2308a5c] + FASTX v2.1.7 [46192b85] + GPUArraysCore v0.2.0 [076d061b] + HashArrayMappedTries v0.2.0 [63c18a36] + KernelAbstractions v0.9.42 [1914dd2f] + MacroTools v0.5.16 [872c559c] + NNlib v0.9.44 [0b1bfda6] + OneHotArrays v0.2.11 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [ae029012] + Requires v1.3.1 [7e506255] + ScopedValues v1.6.2 [90137ffa] + StaticArrays v1.9.19 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 ⌅ [354b36f9] + StringViews v1.3.7 [3bb67fe8] + TranscodingStreams v0.11.3 [013be700] + UnsafeAtomics v0.3.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [4536629a] + OpenBLAS_jll v0.3.34+0 [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 3.54s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 3.6 s ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 2.7 s ✓ MacroTools 0.5 s ✓ Adapt 0.7 s ✓ Statistics 0.6 s ✓ StaticArraysCore 2.7 s ✓ UnsafeAtomics 0.6 s ✓ HashArrayMappedTries 0.7 s ✓ StringViews 0.6 s ✓ ArgCheck 0.8 s ✓ TranscodingStreams 0.6 s ✓ Requires 0.8 s ✓ GZip 2.1 s ✓ ProgressMeter 0.9 s ✓ BFloat16s 1.4 s ✓ StructUtils 0.6 s ✓ Compat 1.0 s ✓ Preferences 0.5 s ✓ GPUArraysCore 0.6 s ✓ Atomix 0.4 s ✓ ScopedValues 0.6 s ✓ BioGenerics 0.5 s ✓ FastaIO 0.7 s ✓ StructUtils → StructUtilsStaticArraysCoreExt 0.4 s ✓ Compat → CompatLinearAlgebraExt 1.2 s ✓ PrecompileTools 0.8 s ✓ DCAUtils 1.6 s ✓ ChainRulesCore 4.6 s ✓ Aqua 10.8 s ✓ StaticArrays 12.6 s ✓ Automa 7.8 s ✓ Parsers 1.0 s ✓ StaticArrays → StaticArraysStatisticsExt 1.1 s ✓ StaticArrays → StaticArraysChainRulesCoreExt 1.0 s ✓ Adapt → AdaptStaticArraysExt 12.9 s ✓ FASTX 6.9 s ✓ JSON 6.2 s ✓ KernelAbstractions 8.0 s ✓ BenchmarkTools 1.5 s ✓ KernelAbstractions → LinearAlgebraExt 9.6 s ✓ NNlib 2.6 s ✓ OneHotArrays 4.7 s ✓ BioSequenceMappings 41 dependencies successfully precompiled in 116 seconds. 32 already precompiled. Precompilation completed after 132.35s ################################################################################ # Testing # Testing BioSequenceMappings Status `/tmp/jl_nIkpSd/Project.toml` [4c88cf16] Aqua v0.8.16 [6e4b80f9] BenchmarkTools v1.8.0 [a84bc454] BioSequenceMappings v0.1.7 [e41cd558] DCAUtils v1.1.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_nIkpSd/Manifest.toml` [79e6a3ab] Adapt v4.7.0 [4c88cf16] Aqua v0.8.16 [dce04be8] ArgCheck v2.5.0 [a9b6321e] Atomix v1.1.3 [67c07d97] Automa v1.2.0 [ab4f0b2a] BFloat16s v0.6.1 [6e4b80f9] BenchmarkTools v1.8.0 [47718e42] BioGenerics v0.1.5 [a84bc454] BioSequenceMappings v0.1.7 [d360d2e6] ChainRulesCore v1.26.1 [34da2185] Compat v4.18.1 [e41cd558] DCAUtils v1.1.0 [c2308a5c] FASTX v2.1.7 [a0c94c4b] FastaIO v1.1.0 [46192b85] GPUArraysCore v0.2.0 ⌅ [92fee26a] GZip v0.6.2 [076d061b] HashArrayMappedTries v0.2.0 [682c06a0] JSON v1.7.1 [63c18a36] KernelAbstractions v0.9.42 [1914dd2f] MacroTools v0.5.16 [872c559c] NNlib v0.9.44 [0b1bfda6] OneHotArrays v0.2.11 ⌅ [69de0a69] Parsers v2.8.7 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [92933f4c] ProgressMeter v1.11.0 [ae029012] Requires v1.3.1 [7e506255] ScopedValues v1.6.2 [90137ffa] StaticArrays v1.9.19 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 ⌅ [354b36f9] StringViews v1.3.7 [ec057cc2] StructUtils v2.8.5 [3bb67fe8] TranscodingStreams v0.11.3 [013be700] UnsafeAtomics v0.3.2 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.12.0 [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 [9abbd945] Profile v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets 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 v1.5.7+0 [deac9b47] LibCURL_jll v8.21.0+0 [e37daf67] LibGit2_jll v1.9.7+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [458c3c95] OpenSSL_jll v3.5.8+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 v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... # Alphabet # Alignment ┌ Warning: I should write a test for `find_sequence` and `match_sequences` └ @ Main ~/.julia/packages/BioSequenceMappings/qk3CM/test/alignments/methods.jl:16 # IO [ Info: Tests: warning will be produced below ┌ Warning: Could not find a default alphabet for characters ['-', '.', 'A', 'C', 'G'] │ Using Alphabet{Char,Int64}: ['-', '.', 'A', 'C', 'G'] └ @ BioSequenceMappings ~/.julia/packages/BioSequenceMappings/qk3CM/src/IO.jl:62 Test Summary: | Pass Total Time BioSequenceMappings.jl | 165 165 38.9s Unbound type parameters detected: [1] var"#Alphabet#20"(kwargs::Base.Pairs{Symbol, V, Nothing, NT} where {V, NT<:NamedTuple}, ::Type{Alphabet}, characters::AbstractVector{<:A}, ::Type{I}) where {A, I<:Integer} @ BioSequenceMappings ~/.julia/packages/BioSequenceMappings/qk3CM/src/alphabet.jl:174 Unbound type parameters: Test Failed at /home/pkgeval/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:38 Expression: isempty(unbounds) Evaluated: isempty(Method[var"#Alphabet#20"(kwargs::Base.Pairs{Symbol, V, Nothing, NT} where {V, NT<:NamedTuple}, ::Type{Alphabet}, characters::AbstractVector{<:A}, ::Type{I}) where {A, I<:Integer} @ BioSequenceMappings ~/.julia/packages/BioSequenceMappings/qk3CM/src/alphabet.jl:174]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] [2] test_unbound_args(m::Module; broken::Bool) @ Aqua ~/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:38 [3] test_unbound_args(m::Module) @ Aqua ~/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:14 [inlined] [4] macro expansion @ ~/.julia/packages/Aqua/h1qD0/src/Aqua.jl:78 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [6] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/h1qD0/src/Aqua.jl:78 Test Summary: | Pass Fail Total Time Aqua.jl | 10 1 11 1m04.4s Method ambiguity | 1 1 7.6s Unbound type parameters | 1 1 12.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.3s Stale dependencies | 1 1 5.2s Compat bounds | 4 4 0.5s Piracy | 1 1 0.3s Persistent tasks | 1 1 25.8s RNG of the outermost testset: Xoshiro(0xf9ebe49bc08139f0, 0x2dfd880118d1333d, 0xc7bbac04ac349c1d, 0x06a52eeaac98e1c1, 0x99132121202a0c7f) ERROR: LoadError: Some tests did not pass: 10 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BioSequenceMappings/qk3CM/test/Aqua.jl:2 in expression starting at /home/pkgeval/.julia/packages/BioSequenceMappings/qk3CM/test/runtests.jl:23 Testing failed after 116.29s ERROR: LoadError: Package BioSequenceMappings 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:3283 [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 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 294.87s: package has test failures