Package evaluation to test SequenceVariation on Julia 1.14.0-DEV.2226 (797a5ef2b0*) started at 2026-05-23T19:41:50.446 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.74s ################################################################################ # Installation # Installing SequenceVariation... Resolving package versions... Installed Twiddle ──────────── v1.1.2 Installed BioGenerics ──────── v0.1.5 Installed BioAlignments ────── v3.1.0 Installed BioSequences ─────── v3.5.1 Installed Preferences ──────── v1.5.2 Installed IntervalTrees ────── v1.1.0 Installed BioSymbols ───────── v5.2.0 Installed TranscodingStreams ─ v0.11.3 Installed SequenceVariation ── v0.2.2 Installed PrecompileTools ──── v1.3.4 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 v1.13.0 [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 v1.5.1+0 [4536629a] + OpenBLAS_jll v0.3.33+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Installation completed after 4.56s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 5.4 s ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 0.8 s ✓ Twiddle 103.8 s ✓ IntervalTrees 58.1 s ✓ TranscodingStreams 1.4 s ✓ Compat 2.3 s ✓ Preferences 42.0 s ✓ BioGenerics 0.6 s ✓ Compat → CompatLinearAlgebraExt 2.4 s ✓ PrecompileTools 44.5 s ✓ Aqua 111.6 s ✓ BioSymbols 111.1 s ✓ BioSequences ┌ Info: JuliaLowering threw given input: │ code = │ :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 =# Core.@doc "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" struct Alignment │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:15 =# │ anchors::Vector{AlignmentAnchor} │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:16 =# │ firstref::Int │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:17 =# │ lastref::Int │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =# │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =# @doc (" Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n"->begin │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =# │ function Alignment(anchors::Vector{AlignmentAnchor}, check::Bool = true) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:25 =# │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:27 =# │ if check │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:28 =# │ check_alignment_anchors(anchors) │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:32 =# │ firstref = 0 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:33 =# │ for i = 1:length(anchors) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:34 =# │ if ismatchop((anchors[i]).op) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:35 =# │ firstref = (anchors[i - 1]).refpos + 1 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:36 =# │ break │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:38 =# │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:40 =# │ lastref = 0 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:41 =# │ for i = length(anchors):-1:1 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:42 =# │ if ismatchop((anchors[i]).op) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:43 =# │ lastref = (anchors[i]).refpos │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:44 =# │ break │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:46 =# │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:48 =# │ return new(anchors, firstref, lastref) │ end │ end) │ end) │ st0 = │ SyntaxTree with attributes mod,kind,var_id,toplevel_pure,scope_type,macro_source,name_val,syntax_flags,meta,scope_layer,value,jl_source,is_toplevel_thunk,source,__macro_ctx__ │ [macrocall] │ │ @doc :: Identifier │ mod │ :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 =#) :: Value │ │ "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" :: Value │ │ [struct] │ │ false :: Value │ │ Alignment :: Identifier │ │ [block] │ │ [::] │ │ anchors :: Identifier │ │ [curly] │ │ Vector :: Identifier │ │ AlignmentAnchor :: Identifier │ │ [::] │ │ firstref :: Identifier │ │ Int :: Identifier │ │ [::] │ │ lastref :: Identifier │ │ Int :: Identifier │ │ [macrocall] │ │ @doc :: Identifier │ │ :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =#) :: Value │ │ [->] │ │ " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n" :: Value │ │ [block] │ │ [function] │ │ [call] │ │ Alignment :: Identifier │ │ [::] │ │ anchors :: Identifier │ │ [curly] │ │ Vector :: Identifier │ │ AlignmentAnchor :: Identifier │ │ [kw] │ │ [::] │ │ check :: Identifier │ │ Bool :: Identifier │ │ true :: Value │ │ [block] │ │ [if] │ │ check :: Identifier │ │ [block] │ │ [call] │ │ check_alignment_anchors :: Identifier │ │ anchors :: Identifier │ │ [=] │ │ firstref :: Identifier │ │ 0 :: Value │ │ [for] │ │ [=] │ │ i :: Identifier │ │ [call] │ │ : :: Identifier │ │ 1 :: Value │ │ [call] │ │ length :: Identifier │ │ anchors :: Identifier │ │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ i :: Identifier │ │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ firstref :: Identifier │ │ [call] │ │ + :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ [call] │ │ - :: Identifier │ │ i :: Identifier │ │ 1 :: Value │ │ [inert] │ │ refpos :: Identifier │ │ 1 :: Value │ │ [break] │ │ [=] │ │ lastref :: Identifier │ │ 0 :: Value │ │ [for] │ │ [=] │ │ i :: Identifier │ │ [call] │ │ : :: Identifier │ │ [call] │ │ length :: Identifier │ │ anchors :: Identifier │ │ -1 :: Value │ │ 1 :: Value │ │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ i :: Identifier │ │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ lastref :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ i :: Identifier │ │ [inert] │ │ refpos :: Identifier │ │ [break] │ │ [return] │ │ [call] │ │ new :: Identifier │ │ anchors :: Identifier │ │ firstref :: Identifier │ │ lastref :: Identifier │ │ │ st1 = │ SyntaxTree with attributes mod,kind,var_id,toplevel_pure,scope_type,macro_source,name_val,syntax_flags,meta,scope_layer,value,jl_source,is_toplevel_thunk,source │ [block] │ │ [=] │ │ val :: Identifier │ scope_layer=3 │ [struct] │ │ false :: Value │ macro_source=122 │ Alignment :: Identifier │ scope_layer=1 │ [block] │ │ [::] │ │ anchors :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ [::] │ │ firstref :: Identifier │ scope_layer=1 │ Int :: Identifier │ scope_layer=1 │ [::] │ │ lastref :: Identifier │ scope_layer=1 │ Int :: Identifier │ scope_layer=1 │ [block] │ │ [block] │ │ [=] │ │ #1#val :: Identifier │ scope_layer=1 │ [function] │ │ [call] │ │ Alignment :: Identifier │ scope_layer=1 │ [::] │ │ anchors :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ [kw] │ │ [::] │ │ check :: Identifier │ scope_layer=1 │ Bool :: Identifier │ scope_layer=1 │ true :: Value │ macro_source=122 │ [block] │ │ [if] │ │ check :: Identifier │ scope_layer=1 │ [block] │ │ [call] │ │ check_alignment_anchors :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ [=] │ │ firstref :: Identifier │ scope_layer=1 │ 0 :: Value │ macro_source=122 │ [for] │ │ [=] │ │ i :: Identifier │ scope_layer=1 │ [call] │ │ : :: Identifier │ scope_layer=1 │ 1 :: Value │ macro_source=122 │ [call] │ │ length :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ firstref :: Identifier │ scope_layer=1 │ [call] │ │ + :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ [call] │ │ - :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ 1 :: Value │ macro_source=122 │ [inert] │ │ refpos :: Identifier │ │ 1 :: Value │ macro_source=122 │ [break] │ macro_source=122 │ [=] │ │ lastref :: Identifier │ scope_layer=1 │ 0 :: Value │ macro_source=122 │ [for] │ │ [=] │ │ i :: Identifier │ scope_layer=1 │ [call] │ │ : :: Identifier │ scope_layer=1 │ [call] │ │ length :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ -1 :: Value │ macro_source=122 │ 1 :: Value │ macro_source=122 │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ lastref :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ [inert] │ │ refpos :: Identifier │ │ [break] │ macro_source=122 │ [return] │ │ [call] │ │ new :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ firstref :: Identifier │ scope_layer=1 │ lastref :: Identifier │ scope_layer=1 │ [call] │ │ Base.Docs.doc! :: Value │ macro_source=122 │ BioAlignments :: Value │ macro_source=122 │ [call] │ │ Base.Docs.Binding :: Value │ macro_source=122 │ BioAlignments :: Value │ macro_source=122 │ [inert] │ │ Alignment :: Identifier │ │ [call] │ macro_source=122 │ Base.Docs.docstr :: Value │ macro_source=122 │ [call] │ macro_source=122 │ Core.svec :: Value │ macro_source=122 │ " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n" :: Value │ macro_source=122 │ [call] │ macro_source=122 │ Dict{Symbol, Any} :: Value │ macro_source=122 │ :path => "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" :: Value │ macro_source=122 │ :linenumber => 20 :: Value │ macro_source=122 │ :module => BioAlignments :: Value │ macro_source=122 │ [curly] │ │ Union :: Identifier │ scope_layer=1 │ [curly] │ │ Tuple :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ [curly] │ │ Tuple :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ Bool :: Identifier │ scope_layer=1 │ #1#val :: Identifier │ scope_layer=1 │ [call] │ │ Base.Docs.doc! :: Value │ macro_source=122 │ BioAlignments :: Value │ macro_source=122 │ [call] │ │ Base.Docs.Binding :: Value │ macro_source=122 │ BioAlignments :: Value │ │ [inert] │ jl_source=L65 │ Alignment :: Identifier │ │ [call] │ │ Base.Docs.docstr :: Value │ macro_source=122 │ [call] │ macro_source=122 │ Core.svec :: Value │ macro_source=122 │ "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" :: Value │ macro_source=122 │ [call] │ │ Dict{Symbol, Any} :: Value │ macro_source=122 │ :path => "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" :: Value │ macro_source=122 │ :linenumber => 9 :: Value │ macro_source=122 │ :module => BioAlignments :: Value │ macro_source=122 │ [call] │ │ Pair :: Value │ macro_source=122 │ [inert] │ │ fields :: Identifier │ │ [call] │ macro_source=122 │ Dict{Symbol, Any} :: Value │ macro_source=122 │ [curly] │ │ Union :: Identifier │ scope_layer=1 │ val :: Identifier │ scope_layer=3 │ │ file = "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" │ line = 9 └ mod = BioAlignments ERROR: LoadError: LoweringError: #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:25 =# - assignment syntax in structure fields is reserved Expression:  (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (iteration (in i (call : 1 (call length anchors)))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= firstref (call + (. (ref anchors (call - i 1)) :refpos) 1)) (break))))) (= lastref 0) (for (iteration (in i (call : (call length anchors) -1 1))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= lastref (. (ref anchors i) :refpos)) (break))))) (return (call new anchors firstref lastref))))) Containing expressions:  (block (:: anchors (curly Vector AlignmentAnchor)) (:: firstref Int) (:: lastref Int) (block (block (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (iteration (in i (call : 1 (call length anchors)))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= firstref (call + (. (ref anchors (call - i 1)) :refpos) 1)) (break))))) (= lastref 0) (for (iteration (in i (call : (call length anchors) -1 1))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= lastref (. (ref anchors i) :refpos)) (break))))) (return (call new anchors firstref lastref))))) (call Base.Docs.doc! BioAlignments (call Base.Docs.Binding BioAlignments :Alignment) (call Base.Docs.docstr (call Core.svec " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n") (call Dict{Symbol, Any} :path => "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" :linenumber => 20 :module => BioAlignments)) (curly Union (curly Tuple (curly Vector AlignmentAnchor)) (curly Tuple (curly Vector AlignmentAnchor) Bool))) #1#val)))  Detailed provenance:  (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (iteration (in i (call : 1 (call length anchors)))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= firstref (call + (. (ref anchors (call - i 1)) :refpos) 1)) (break))))) (= lastref 0) (for (iteration (in i (call : (call length anchors) -1 1))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= lastref (. (ref anchors i) :refpos)) (break))))) (return (call new anchors firstref lastref)))))  └─ (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (= i (call : 1 (call length anchors))) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= firstref (call + (. (ref anchors (call - i 1)) (inert refpos)) 1)) (break))))) (= lastref 0) (for (= i (call : (call length anchors) -1 1)) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= lastref (. (ref anchors i) (inert refpos))) (break))))) (return (call new anchors firstref lastref)))))  └─ (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (= i (call : 1 (call length anchors))) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= firstref (call + (. (ref anchors (call - i 1)) (inert refpos)) 1)) (break))))) (= lastref 0) (for (= i (call : (call length anchors) -1 1)) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= lastref (. (ref anchors i) (inert refpos))) (break))))) (return (call new anchors firstref lastref)))))  ├─ @ /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:25  └─ (macrocall @doc :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 =#) "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" (struct false Alignment (block (:: anchors (curly Vector AlignmentAnchor)) (:: firstref Int) (:: lastref Int) (macrocall @doc :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =#) (-> " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n" (block (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (= i (call : 1 (call length anchors))) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= firstref (call + (. (ref anchors (call - i 1)) (inert refpos)) 1)) (break))))) (= lastref 0) (for (= i (call : (call length anchors) -1 1)) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= lastref (. (ref anchors i) (inert refpos))) (break))))) (return (call new anchors firstref lastref))))))))))  └─ @ /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9  Stacktrace:  [1] _collect_struct_fields(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, field_names::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_types::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_attrs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_docs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, inner_defs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, exs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, SubArray{Int64, 1, Vector{Int64}, Tuple{UnitRange{Int64}}, true}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:3184  ┌ [2] _collect_struct_fields(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, field_names::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_types::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_attrs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_docs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, inner_defs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, exs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, SubArray{Int64, 1, Vector{Int64}, Tuple{UnitRange{Int64}}, true}})  │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:3181  ╰──── repeated 2 times  [4] expand_struct_def(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:3754  [5] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4336  [6] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4152  [7] expand_assignment(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, is_const::Bool)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:1318  [8] expand_assignment(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:1268  [9] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4196  [10] expand_forms_2  @ /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4152 [inlined]  [11] #expand_forms_2##2  @ /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4440 [inlined]  [12] mapchildren(f::Base.JuliaLowering.var"#expand_forms_2##2#expand_forms_2##3"{Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}}, ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaSyntax /source/usr/share/julia/JuliaSyntax/src/porcelain/syntax_graph.jl:707  [13] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4440  [14] Dict{Int64, Int64}()  @ Base /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4152 [inlined]  [15] expand_forms_2(ctx::Base.JuliaLowering.MacroExpansionContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4469  [16] core_lowering_hook(code::Any, mod::Module, file::String, line::UInt64, world::UInt64, _warn::Bool)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/hooks.jl:30  [17] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:327  [18] top-level scope  @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:93  [19] include(mod::Module, _path::String)  @ Base ./Base.jl:326  [20] 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:3271  [21] top-level scope  @ stdin:5  [22] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3113  [24] push!(a::Vector{SubString{String}}, item::String)  @ Base ./loading.jl:3123 [inlined]  [25] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:353  [26] _start()  @ Base ./client.jl:596 in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:3 in expression starting at stdin:5 ✗ BioAlignments ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("00701ae9-d1dc-5365-b64a-a3a3ebf5695e"), "BioAlignments") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base ./error.jl:56  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2818  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2672  [4] macro expansion  @ ./loading.jl:2599 [inlined]  [5] string(::String, ::Union{Char, SubString{String}, String, Symbol}, ::Symbol, ::String)  @ Base ./lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2563  [7] require  @ ./loading.jl:2539 [inlined]  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)  @ Base ./module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base ./module.jl:101  [11] eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:195  [12] top-level scope  @ ~/.julia/packages/SequenceVariation/y7qGk/src/SequenceVariation.jl:23  [13] include(mod::Module, _path::String)  @ Base ./Base.jl:326  [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:3271  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3113  [18] push!(a::Vector{SubString{String}}, item::String)  @ Base ./loading.jl:3123 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:353  [20] _start()  @ Base ./client.jl:596 in expression starting at /home/pkgeval/.julia/packages/SequenceVariation/y7qGk/src/SequenceVariation.jl:1 in expression starting at stdin:5 ✗ SequenceVariation 11 dependencies successfully precompiled in 574 seconds. 30 already precompiled. Precompilation completed after 605.14s ################################################################################ # Testing # Testing SequenceVariation Status `/tmp/jl_o0qGQc/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_o0qGQc/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 v1.13.0 [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 v1.5.1+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.3+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... ┌ Info: JuliaLowering threw given input: │ code = │ :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 =# Core.@doc "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" struct Alignment │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:15 =# │ anchors::Vector{AlignmentAnchor} │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:16 =# │ firstref::Int │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:17 =# │ lastref::Int │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =# │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =# @doc (" Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n"->begin │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =# │ function Alignment(anchors::Vector{AlignmentAnchor}, check::Bool = true) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:25 =# │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:27 =# │ if check │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:28 =# │ check_alignment_anchors(anchors) │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:32 =# │ firstref = 0 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:33 =# │ for i = 1:length(anchors) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:34 =# │ if ismatchop((anchors[i]).op) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:35 =# │ firstref = (anchors[i - 1]).refpos + 1 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:36 =# │ break │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:38 =# │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:40 =# │ lastref = 0 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:41 =# │ for i = length(anchors):-1:1 │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:42 =# │ if ismatchop((anchors[i]).op) │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:43 =# │ lastref = (anchors[i]).refpos │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:44 =# │ break │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:46 =# │ end │ #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:48 =# │ return new(anchors, firstref, lastref) │ end │ end) │ end) │ st0 = │ SyntaxTree with attributes mod,kind,var_id,toplevel_pure,scope_type,macro_source,name_val,syntax_flags,meta,scope_layer,value,jl_source,is_toplevel_thunk,source,__macro_ctx__ │ [macrocall] │ │ @doc :: Identifier │ mod │ :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 =#) :: Value │ │ "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" :: Value │ │ [struct] │ │ false :: Value │ │ Alignment :: Identifier │ │ [block] │ │ [::] │ │ anchors :: Identifier │ │ [curly] │ │ Vector :: Identifier │ │ AlignmentAnchor :: Identifier │ │ [::] │ │ firstref :: Identifier │ │ Int :: Identifier │ │ [::] │ │ lastref :: Identifier │ │ Int :: Identifier │ │ [macrocall] │ │ @doc :: Identifier │ │ :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =#) :: Value │ │ [->] │ │ " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n" :: Value │ │ [block] │ │ [function] │ │ [call] │ │ Alignment :: Identifier │ │ [::] │ │ anchors :: Identifier │ │ [curly] │ │ Vector :: Identifier │ │ AlignmentAnchor :: Identifier │ │ [kw] │ │ [::] │ │ check :: Identifier │ │ Bool :: Identifier │ │ true :: Value │ │ [block] │ │ [if] │ │ check :: Identifier │ │ [block] │ │ [call] │ │ check_alignment_anchors :: Identifier │ │ anchors :: Identifier │ │ [=] │ │ firstref :: Identifier │ │ 0 :: Value │ │ [for] │ │ [=] │ │ i :: Identifier │ │ [call] │ │ : :: Identifier │ │ 1 :: Value │ │ [call] │ │ length :: Identifier │ │ anchors :: Identifier │ │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ i :: Identifier │ │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ firstref :: Identifier │ │ [call] │ │ + :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ [call] │ │ - :: Identifier │ │ i :: Identifier │ │ 1 :: Value │ │ [inert] │ │ refpos :: Identifier │ │ 1 :: Value │ │ [break] │ │ [=] │ │ lastref :: Identifier │ │ 0 :: Value │ │ [for] │ │ [=] │ │ i :: Identifier │ │ [call] │ │ : :: Identifier │ │ [call] │ │ length :: Identifier │ │ anchors :: Identifier │ │ -1 :: Value │ │ 1 :: Value │ │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ i :: Identifier │ │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ lastref :: Identifier │ │ [.] │ │ [ref] │ │ anchors :: Identifier │ │ i :: Identifier │ │ [inert] │ │ refpos :: Identifier │ │ [break] │ │ [return] │ │ [call] │ │ new :: Identifier │ │ anchors :: Identifier │ │ firstref :: Identifier │ │ lastref :: Identifier │ │ │ st1 = │ SyntaxTree with attributes mod,kind,var_id,toplevel_pure,scope_type,macro_source,name_val,syntax_flags,meta,scope_layer,value,jl_source,is_toplevel_thunk,source │ [block] │ │ [=] │ │ val :: Identifier │ scope_layer=3 │ [struct] │ │ false :: Value │ macro_source=122 │ Alignment :: Identifier │ scope_layer=1 │ [block] │ │ [::] │ │ anchors :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ [::] │ │ firstref :: Identifier │ scope_layer=1 │ Int :: Identifier │ scope_layer=1 │ [::] │ │ lastref :: Identifier │ scope_layer=1 │ Int :: Identifier │ scope_layer=1 │ [block] │ │ [block] │ │ [=] │ │ #1#val :: Identifier │ scope_layer=1 │ [function] │ │ [call] │ │ Alignment :: Identifier │ scope_layer=1 │ [::] │ │ anchors :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ [kw] │ │ [::] │ │ check :: Identifier │ scope_layer=1 │ Bool :: Identifier │ scope_layer=1 │ true :: Value │ macro_source=122 │ [block] │ │ [if] │ │ check :: Identifier │ scope_layer=1 │ [block] │ │ [call] │ │ check_alignment_anchors :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ [=] │ │ firstref :: Identifier │ scope_layer=1 │ 0 :: Value │ macro_source=122 │ [for] │ │ [=] │ │ i :: Identifier │ scope_layer=1 │ [call] │ │ : :: Identifier │ scope_layer=1 │ 1 :: Value │ macro_source=122 │ [call] │ │ length :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ firstref :: Identifier │ scope_layer=1 │ [call] │ │ + :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ [call] │ │ - :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ 1 :: Value │ macro_source=122 │ [inert] │ │ refpos :: Identifier │ │ 1 :: Value │ macro_source=122 │ [break] │ macro_source=122 │ [=] │ │ lastref :: Identifier │ scope_layer=1 │ 0 :: Value │ macro_source=122 │ [for] │ │ [=] │ │ i :: Identifier │ scope_layer=1 │ [call] │ │ : :: Identifier │ scope_layer=1 │ [call] │ │ length :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ -1 :: Value │ macro_source=122 │ 1 :: Value │ macro_source=122 │ [block] │ │ [if] │ │ [call] │ │ ismatchop :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ [inert] │ │ op :: Identifier │ │ [block] │ │ [=] │ │ lastref :: Identifier │ scope_layer=1 │ [.] │ │ [ref] │ │ anchors :: Identifier │ scope_layer=1 │ i :: Identifier │ scope_layer=1 │ [inert] │ │ refpos :: Identifier │ │ [break] │ macro_source=122 │ [return] │ │ [call] │ │ new :: Identifier │ scope_layer=1 │ anchors :: Identifier │ scope_layer=1 │ firstref :: Identifier │ scope_layer=1 │ lastref :: Identifier │ scope_layer=1 │ [call] │ │ Base.Docs.doc! :: Value │ macro_source=122 │ BioAlignments :: Value │ macro_source=122 │ [call] │ │ Base.Docs.Binding :: Value │ macro_source=122 │ BioAlignments :: Value │ macro_source=122 │ [inert] │ │ Alignment :: Identifier │ │ [call] │ macro_source=122 │ Base.Docs.docstr :: Value │ macro_source=122 │ [call] │ macro_source=122 │ Core.svec :: Value │ macro_source=122 │ " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n" :: Value │ macro_source=122 │ [call] │ macro_source=122 │ Dict{Symbol, Any} :: Value │ macro_source=122 │ :path => "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" :: Value │ macro_source=122 │ :linenumber => 20 :: Value │ macro_source=122 │ :module => BioAlignments :: Value │ macro_source=122 │ [curly] │ │ Union :: Identifier │ scope_layer=1 │ [curly] │ │ Tuple :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ [curly] │ │ Tuple :: Identifier │ scope_layer=1 │ [curly] │ │ Vector :: Identifier │ scope_layer=1 │ AlignmentAnchor :: Identifier │ scope_layer=1 │ Bool :: Identifier │ scope_layer=1 │ #1#val :: Identifier │ scope_layer=1 │ [call] │ │ Base.Docs.doc! :: Value │ macro_source=122 │ BioAlignments :: Value │ macro_source=122 │ [call] │ │ Base.Docs.Binding :: Value │ macro_source=122 │ BioAlignments :: Value │ │ [inert] │ jl_source=L65 │ Alignment :: Identifier │ │ [call] │ │ Base.Docs.docstr :: Value │ macro_source=122 │ [call] │ macro_source=122 │ Core.svec :: Value │ macro_source=122 │ "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" :: Value │ macro_source=122 │ [call] │ │ Dict{Symbol, Any} :: Value │ macro_source=122 │ :path => "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" :: Value │ macro_source=122 │ :linenumber => 9 :: Value │ macro_source=122 │ :module => BioAlignments :: Value │ macro_source=122 │ [call] │ │ Pair :: Value │ macro_source=122 │ [inert] │ │ fields :: Identifier │ │ [call] │ macro_source=122 │ Dict{Symbol, Any} :: Value │ macro_source=122 │ [curly] │ │ Union :: Identifier │ scope_layer=1 │ val :: Identifier │ scope_layer=3 │ │ file = "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" │ line = 9 └ mod = BioAlignments ERROR: LoadError: LoweringError: #= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:25 =# - assignment syntax in structure fields is reserved Expression:  (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (iteration (in i (call : 1 (call length anchors)))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= firstref (call + (. (ref anchors (call - i 1)) :refpos) 1)) (break))))) (= lastref 0) (for (iteration (in i (call : (call length anchors) -1 1))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= lastref (. (ref anchors i) :refpos)) (break))))) (return (call new anchors firstref lastref))))) Containing expressions:  (block (:: anchors (curly Vector AlignmentAnchor)) (:: firstref Int) (:: lastref Int) (block (block (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (iteration (in i (call : 1 (call length anchors)))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= firstref (call + (. (ref anchors (call - i 1)) :refpos) 1)) (break))))) (= lastref 0) (for (iteration (in i (call : (call length anchors) -1 1))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= lastref (. (ref anchors i) :refpos)) (break))))) (return (call new anchors firstref lastref))))) (call Base.Docs.doc! BioAlignments (call Base.Docs.Binding BioAlignments :Alignment) (call Base.Docs.docstr (call Core.svec " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n") (call Dict{Symbol, Any} :path => "/home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl" :linenumber => 20 :module => BioAlignments)) (curly Union (curly Tuple (curly Vector AlignmentAnchor)) (curly Tuple (curly Vector AlignmentAnchor) Bool))) #1#val)))  Detailed provenance:  (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (iteration (in i (call : 1 (call length anchors)))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= firstref (call + (. (ref anchors (call - i 1)) :refpos) 1)) (break))))) (= lastref 0) (for (iteration (in i (call : (call length anchors) -1 1))) (block (if (call ismatchop (. (ref anchors i) :op)) (block (= lastref (. (ref anchors i) :refpos)) (break))))) (return (call new anchors firstref lastref)))))  └─ (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (= i (call : 1 (call length anchors))) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= firstref (call + (. (ref anchors (call - i 1)) (inert refpos)) 1)) (break))))) (= lastref 0) (for (= i (call : (call length anchors) -1 1)) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= lastref (. (ref anchors i) (inert refpos))) (break))))) (return (call new anchors firstref lastref)))))  └─ (= #1#val (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (= i (call : 1 (call length anchors))) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= firstref (call + (. (ref anchors (call - i 1)) (inert refpos)) 1)) (break))))) (= lastref 0) (for (= i (call : (call length anchors) -1 1)) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= lastref (. (ref anchors i) (inert refpos))) (break))))) (return (call new anchors firstref lastref)))))  ├─ @ /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:25  └─ (macrocall @doc :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 =#) "Defines how to align a given sequence onto a reference sequence.\nThe alignment is represented as a sequence of elementary operations (match, insertion, deletion etc)\nanchored to specific positions of the input and reference sequence.\n" (struct false Alignment (block (:: anchors (curly Vector AlignmentAnchor)) (:: firstref Int) (:: lastref Int) (macrocall @doc :(#= /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:20 =#) (-> " Alignment(anchors::Vector{AlignmentAnchor}, check=true)\n\nCreate an alignment object from a sequence of alignment anchors.\n" (block (function (call Alignment (:: anchors (curly Vector AlignmentAnchor)) (kw (:: check Bool) true)) (block (if check (block (call check_alignment_anchors anchors))) (= firstref 0) (for (= i (call : 1 (call length anchors))) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= firstref (call + (. (ref anchors (call - i 1)) (inert refpos)) 1)) (break))))) (= lastref 0) (for (= i (call : (call length anchors) -1 1)) (block (if (call ismatchop (. (ref anchors i) (inert op))) (block (= lastref (. (ref anchors i) (inert refpos))) (break))))) (return (call new anchors firstref lastref))))))))))  └─ @ /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9  Stacktrace:  [1] _collect_struct_fields(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, field_names::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_types::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_attrs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_docs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, inner_defs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, exs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, SubArray{Int64, 1, Vector{Int64}, Tuple{UnitRange{Int64}}, true}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:3184  ┌ [2] _collect_struct_fields(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, field_names::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_types::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_attrs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, field_docs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, inner_defs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, Vector{Int64}}, exs::Base.JuliaSyntax.SyntaxList{Dict{Symbol, Dict{Int64, Any}}, SubArray{Int64, 1, Vector{Int64}, Tuple{UnitRange{Int64}}, true}})  │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:3181  ╰──── repeated 2 times  [4] expand_struct_def(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:3754  [5] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4336  [6] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4152  [7] expand_assignment(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, is_const::Bool)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:1318  [8] expand_assignment(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:1268  [9] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4196  [10] expand_forms_2  @ /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4152 [inlined]  [11] #expand_forms_2##2  @ /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4440 [inlined]  [12] mapchildren(f::Base.JuliaLowering.var"#expand_forms_2##2#expand_forms_2##3"{Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}}, ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaSyntax /source/usr/share/julia/JuliaSyntax/src/porcelain/syntax_graph.jl:707  [13] expand_forms_2(ctx::Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}, docs::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4440  [14] Dict{Int64, Int64}()  @ Base /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4152 [inlined]  [15] expand_forms_2(ctx::Base.JuliaLowering.MacroExpansionContext{Dict{Symbol, Dict{Int64, Any}}}, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4469  [16] core_lowering_hook(code::Any, mod::Module, file::String, line::UInt64, world::UInt64, _warn::Bool)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/hooks.jl:30  [17] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:327  [18] top-level scope  @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:93  [19] include(mod::Module, _path::String)  @ Base ./Base.jl:326  [20] 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:3271  [21] top-level scope  @ stdin:5  [22] eval(m::Module, e::Any)  @ Core ./boot.jl:517  [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3113  [24] push!(a::Vector{SubString{String}}, item::String)  @ Base ./loading.jl:3123 [inlined]  [25] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:353  [26] _start()  @ Base ./client.jl:596 in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/alignment.jl:9 in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:3 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ BioAlignments │ [Output was shown above] └ ERROR: LoadError: The following 1 package failed to precompile: BioAlignments Failed to precompile BioAlignments [00701ae9-d1dc-5365-b64a-a3a3ebf5695e] to "/home/pkgeval/.julia/compiled/v1.14/BioAlignments/jl_UkOCiM" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/SequenceVariation/y7qGk/test/runtests.jl:27 Testing failed after 217.69s 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] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3110 [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:587 [5] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:355 [12] _start() @ Base ./client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 871.03s: package fails to precompile