Package evaluation to test VectorizedKmers on Julia 1.14.0-DEV.1441 (812f3beb0a*) started at 2025-12-30T12:22:57.112 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.94s ################################################################################ # Installation # Installing VectorizedKmers... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [2ef45bd6] + VectorizedKmers v0.9.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [1e83bf80] + StaticArraysCore v1.4.4 [2ef45bd6] + VectorizedKmers v0.9.2 Installation completed after 3.83s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 13.45s ################################################################################ # Testing # Testing VectorizedKmers Status `/tmp/jl_Xfgo7R/Project.toml` [7e6ae17a] BioSequences v3.5.0 [1e83bf80] StaticArraysCore v1.4.4 [2ef45bd6] VectorizedKmers v0.9.2 [8dfed614] Test v1.11.0 Status `/tmp/jl_Xfgo7R/Manifest.toml` [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [1e83bf80] StaticArraysCore v1.4.4 [7200193e] Twiddle v1.1.2 [2ef45bd6] VectorizedKmers v0.9.2 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [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 v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [4ec0a83e] Unicode v1.11.0 Testing Running tests... ┌ Warning: The call to compilecache failed to create a usable precompiled cache file for BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] │ exception = Required dependency Base.PkgId(Base.UUID("21216c6a-2e73-6563-6e65-726566657250"), "Preferences") failed to load from a cache file. └ @ Base loading.jl:2950 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2873  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2725  [4] macro expansion  @ ./loading.jl:2653 [inlined]  [5] macro expansion  @ ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2617  [7] require  @ ./loading.jl:2593 [inlined]  [8] eval_import_path  @ ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_using  @ ./module.jl:137 [inlined]  [11] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [12] top-level scope  @ ~/.julia/packages/VectorizedKmers/ReHLs/ext/BioSequencesExt.jl:3  [13] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3309  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3151  [18] include_string  @ ./loading.jl:3161 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [20] _start()  @ Base ./client.jl:585 in expression starting at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/ext/BioSequencesExt.jl:1 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ VectorizedKmers → BioSequencesExt │ [Output was shown above] └ ┌ Error: Error during loading of extension BioSequencesExt of VectorizedKmers, use `Base.retry_load_extensions()` to retry. │ exception = │ 1-element ExceptionStack: │ The following 1 package failed to precompile: │ │ VectorizedKmers → BioSequencesExt │ Failed to precompile BioSequencesExt [5cca929b-467d-5506-8cad-7d53b394aa7f] to "/home/pkgeval/.julia/compiled/v1.14/BioSequencesExt/jl_0DsImD" (ProcessExited(1)). │ └ @ Base loading.jl:1781 count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 Test threw exception Expression: values(count_kmers(dna"ACGT", 1)) == [1, 1, 1, 1] DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSequence{DNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:8 Test threw exception Expression: count_kmers(dna"ACGT", 1) == KmerArray([1, 1, 1, 1]) DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSequence{DNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:8 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:9 Test threw exception Expression: count_kmers(rna"ACGU", 1) == KmerArray([1, 1, 1, 1]) RNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:RNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{RNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSequence{RNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:9 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:10 Test threw exception Expression: count_kmers(view(dna"ACGT", 1:3), 1) == KmerArray([1, 1, 1, 0]) DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSubSeq{DNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:10 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:11 Test threw exception Expression: count_kmers(view(rna"ACGU", 2:4), 1) == KmerArray([0, 1, 1, 1]) RNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:RNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{RNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSubSeq{RNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:11 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:12 Test threw exception Expression: count_kmers(dna"ACGT", 1) == count_kmers(dna"ACGT", 1, UInt) DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSequence{DNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:12 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:13 Test threw exception Expression: count_kmers(dna"ACGT", 1) == count_kmers(LongDNA{2}(dna"ACGT"), 1) DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSequence{DNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:13 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:15 Test threw exception Expression: count_kmers(view(LongDNA{2}(dna"A" ^ 32 * dna"T"), 33:33), 1) == KmerArray([0, 0, 0, 1]) DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSubSeq{DNAAlphabet{2}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:15 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:16 Test threw exception Expression: count_kmers(view(dna"A" ^ 16 * dna"T", 17:17), 1) == KmerArray([0, 0, 0, 1]) DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSubSeq{DNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:16 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:19 Test threw exception Expression: count_kmers!(kv, dna"ACGT") == KmerArray([1, 1, 1, 1]) MethodError: no method matching axis_index(::KmerArray{4, 1, Int64, Vector{Int64}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] #count_kmers!#3 @ ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:12 [inlined] [2] count_kmers!(kmer_array::KmerArray{4, 1, Int64, Vector{Int64}}, sequence::LongSequence{DNAAlphabet{4}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:6 [3] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [5] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [7] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:19 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:20 Test threw exception Expression: kv[LongDNA{2}(dna"A")] == 1 MethodError: no method matching axis_index(::KmerArray{4, 1, Int64, Vector{Int64}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] (::VectorizedKmers.var"#deconstruct##0#deconstruct##1"{KmerArray{4, 1, Int64, Vector{Int64}}})(m::DNA) @ VectorizedKmers ./none:-1 [2] iterate @ ./generator.jl:48 [inlined] [3] getindex(ka::KmerArray{4, 1, Int64, Vector{Int64}}, kmer::LongSequence{DNAAlphabet{2}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:43 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:20 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:21 Test threw exception Expression: kv[dna"A"] == 1 MethodError: no method matching axis_index(::KmerArray{4, 1, Int64, Vector{Int64}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] (::VectorizedKmers.var"#deconstruct##0#deconstruct##1"{KmerArray{4, 1, Int64, Vector{Int64}}})(m::DNA) @ VectorizedKmers ./none:-1 [2] iterate @ ./generator.jl:48 [inlined] [3] getindex(ka::KmerArray{4, 1, Int64, Vector{Int64}}, kmer::LongSequence{DNAAlphabet{4}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:43 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:21 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:24 Test threw exception Expression: count_kmers!(kv, dna"ACGT") == KmerArray([0; 1; 0; 0;; 0; 0; 1; 0;; 0; 0; 0; 1;; 0; 0; 0; 0]) MethodError: no method matching axis_index(::KmerArray{4, 2, Int64, Matrix{Int64}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] #count_kmers!#3 @ ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:12 [inlined] [2] count_kmers!(kmer_array::KmerArray{4, 2, Int64, Matrix{Int64}}, sequence::LongSequence{DNAAlphabet{4}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:6 [3] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [5] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [7] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:24 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:25 Test threw exception Expression: kv[LongDNA{2}(dna"AC")] == 1 MethodError: no method matching axis_index(::KmerArray{4, 2, Int64, Matrix{Int64}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] (::VectorizedKmers.var"#deconstruct##0#deconstruct##1"{KmerArray{4, 2, Int64, Matrix{Int64}}})(m::DNA) @ VectorizedKmers ./none:-1 [2] iterate @ ./generator.jl:48 [inlined] [3] getindex(ka::KmerArray{4, 2, Int64, Matrix{Int64}}, kmer::LongSequence{DNAAlphabet{2}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:43 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:25 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:26 Test threw exception Expression: kv[dna"AC"] == 1 MethodError: no method matching axis_index(::KmerArray{4, 2, Int64, Matrix{Int64}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] (::VectorizedKmers.var"#deconstruct##0#deconstruct##1"{KmerArray{4, 2, Int64, Matrix{Int64}}})(m::DNA) @ VectorizedKmers ./none:-1 [2] iterate @ ./generator.jl:48 [inlined] [3] getindex(ka::KmerArray{4, 2, Int64, Matrix{Int64}}, kmer::LongSequence{DNAAlphabet{4}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:43 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:26 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:29 Test threw exception Expression: all([count_kmers(seq[i:j], 3) == count_kmers(view(seq, i:j), 3) for i = 1:50, j = 1:50]) DNA does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:DNA})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{DNA}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongSequence{DNAAlphabet{4}}, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] (::var"#3#4"{LongSequence{DNAAlphabet{4}}})(::Tuple{Int64, Int64}) @ Main ./none:-1 [5] iterate @ ./generator.jl:48 [inlined] [6] collect(itr::Base.Generator{Base.Iterators.ProductIterator{Tuple{UnitRange{Int64}, UnitRange{Int64}}}, var"#3#4"{LongSequence{DNAAlphabet{4}}}}) @ Base ./array.jl:828 [7] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [9] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [11] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:29 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:31 Test threw exception Expression: values(count_kmers!(KmerArray{4, 5}(falses(4 ^ 5)), seq)) == values(count_kmers(seq, 5)) .% 2 MethodError: no method matching axis_index(::KmerArray{4, 5, Bool, BitArray{5}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] #count_kmers!#3 @ ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:12 [inlined] [2] count_kmers!(kmer_array::KmerArray{4, 5, Bool, BitArray{5}}, sequence::LongSequence{DNAAlphabet{4}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:6 [3] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [5] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [7] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:31 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:32 Test threw exception Expression: values(count_kmers!(KmerArray{4, 5}(falses(4 ^ 5)), view(seq, 1:50))) == values(count_kmers(seq[1:50], 5)) .% 2 MethodError: no method matching axis_index(::KmerArray{4, 5, Bool, BitArray{5}}, ::DNA) The function `axis_index` exists, but no method is defined for this combination of argument types. Closest candidates are: axis_index(::KmerArray, !Matched::Integer) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:37 Stacktrace: [1] #count_kmers!#3 @ ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:12 [inlined] [2] count_kmers!(kmer_array::KmerArray{4, 5, Bool, BitArray{5}}, sequence::LongSubSeq{DNAAlphabet{4}}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:6 [3] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [5] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [7] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:32 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:35 Test threw exception Expression: all((count_kmers(aa_seq[i:j], 2) == count_kmers(view(aa_seq, i:j), 2) for i = 1:50, j = 1:50)) AminoAcid does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:AminoAcid})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{AminoAcid}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongAA, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] (::var"#5#6"{LongAA})(::Tuple{Int64, Int64}) @ Main ./none:-1 [5] iterate @ ./generator.jl:48 [inlined] [6] _all @ ./anyall.jl:210 [inlined] [7] all @ ./anyall.jl:202 [inlined] [8] all(itr::Base.Generator{Base.Iterators.ProductIterator{Tuple{UnitRange{Int64}, UnitRange{Int64}}}, var"#5#6"{LongAA}}) @ Base ./anyall.jl:80 [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/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [12] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [14] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:35 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] count_kmers: Error During Test at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:36 Test threw exception Expression: (count_kmers(aa_seq, 2))[aa"AY"] >= 1 AminoAcid does not have a defined alphabet size. Please define `default_alphabet_size(::Type{<:AminoAcid})` or insert the alphabet size as a second argument in the `count_kmers` function call. Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] default_alphabet_size(::Type{AminoAcid}) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/KmerArray.jl:55 [3] count_kmers(::LongAA, ::Int64) @ VectorizedKmers ~/.julia/packages/VectorizedKmers/ReHLs/src/count.jl:23 [4] top-level scope @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:5 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [6] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:7 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/VectorizedKmers/ReHLs/test/ext/BioSequencesExt.jl:36 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] Test Summary: | Pass Error Total Time VectorizedKmers.jl | 18 20 38 38.8s KmerArray.jl | 14 14 2.6s count.jl | 4 4 0.2s extensions | 20 20 35.4s BioSequencesExt.jl | 20 20 7.5s count_kmers | 20 20 7.5s RNG of the outermost testset: Random.Xoshiro(0xa411b161e9edd097, 0xfb22058a565c81a4, 0x8bba2eddd50801f6, 0x84e5fbc4e27a9e96, 0xf2648eb84785b56b) ERROR: LoadError: Some tests did not pass: 18 passed, 0 failed, 20 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/VectorizedKmers/ReHLs/test/runtests.jl:4 Testing failed after 53.66s ERROR: LoadError: Package VectorizedKmers 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:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [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:237 [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:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 98.89s: package fails to precompile