Package evaluation to load BioRecordsProcessing on Julia 1.14.0-DEV.2309 (6e1a27e459*) started at 2026-06-06T10:33:41.044 ################################################################################ # Set-up # Set-up completed after 0.15s ################################################################################ # Installation # Installing BioRecordsProcessing... Resolving package versions... Installed OrderedCollections ─── v1.8.2 Installed Indexes ────────────── v0.1.3 Installed TranscodingStreams ─── v0.9.13 Installed CodecZlib ──────────── v0.7.8 Installed GenomicFeatures ────── v2.1.0 Installed Glob ───────────────── v1.5.0 Installed Compat ─────────────── v4.18.1 Installed DataStructures ─────── v0.18.22 Installed Twiddle ────────────── v1.1.2 Installed BioAlignments ──────── v3.1.0 Installed Automa ─────────────── v1.1.0 Installed SIMD ───────────────── v3.7.2 Installed BioGenerics ────────── v0.1.5 Installed BioSymbols ─────────── v5.2.0 Installed BioRecordsProcessing ─ v0.2.3 Installed XAM ────────────────── v0.4.2 Installed Preferences ────────── v1.5.2 Installed PrecompileTools ────── v1.3.4 Installed BGZFStreams ────────── v0.3.2 Installed IntervalTrees ──────── v1.1.0 Installed BioSequences ───────── v3.5.1 Updating `~/.julia/environments/v1.14/Project.toml` [321bc2d7] + BioRecordsProcessing v0.2.3 Updating `~/.julia/environments/v1.14/Manifest.toml` [67c07d97] + Automa v1.1.0 [28d598bf] + BGZFStreams v0.3.2 [00701ae9] + BioAlignments v3.1.0 [47718e42] + BioGenerics v0.1.5 [321bc2d7] + BioRecordsProcessing v0.2.3 [7e6ae17a] + BioSequences v3.5.1 [3c28c6f8] + BioSymbols v5.2.0 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 ⌅ [899a7d2d] + GenomicFeatures v2.1.0 [c27321d9] + Glob v1.5.0 ⌅ [4ffb77ac] + Indexes v0.1.3 [524e6230] + IntervalTrees v1.1.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [fdea26ae] + SIMD v3.7.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [7200193e] + Twiddle v1.1.2 [d759349c] + XAM v0.4.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [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 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.2+0 [4536629a] + OpenBLAS_jll v0.3.33+0 [83775a58] + Zlib_jll v1.3.2+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 10.28s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Project No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` Manifest No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling project... 0.9 s ✓ Glob 0.6 s ✓ Twiddle 92.3 s ✓ IntervalTrees 153.6 s ✓ OrderedCollections 2.9 s ✓ Preferences 1.6 s ✓ Compat 93.4 s ✓ TranscodingStreams 3.2 s ✓ PrecompileTools 0.7 s ✓ Compat → CompatLinearAlgebraExt 62.5 s ✓ BioGenerics 41.4 s ✓ CodecZlib 651.4 s ✓ SIMD 108.7 s ✓ BioSymbols 274.3 s ✓ DataStructures 39.4 s ✓ BGZFStreams 212.3 s ✓ Automa 107.1 s ✓ BioSequences 190.2 s ✓ GenomicFeatures ┌ 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) (= #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 (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:3166  [2] 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:3736  [3] 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:4317  [4] 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:4133  [5] 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:1320  [6] 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:1270  [7] 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:4177  [8] 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:4133 [inlined]  [9] (::Base.JuliaLowering.var"#expand_forms_2##2#expand_forms_2##3"{Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}})(e::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4421 [inlined]  [10] 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  [11] 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:4421  [12] 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:4133 [inlined]  [13] 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:4450  [14] 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  [15] include(mapexpr::Function, mod::Module, _path::String)  @ Base Base.jl:327  [16] top-level scope  @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:93  [17] include(mod::Module, _path::String)  @ Base Base.jl:326  [18] 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:3296  [19] top-level scope  @ stdin:5  [20] eval(m::Module, e::Any)  @ Core boot.jl:521  [21] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [22] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [23] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [24] _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 127.4 s ✓ Indexes 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:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base loading.jl:2539 [inlined]  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)  @ Base module.jl:36 [inlined]  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)  @ Base module.jl:111  [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:195  [11] top-level scope  @ ~/.julia/packages/XAM/gm2PK/src/sam/sam.jl:8  [12] include(mapexpr::Function, mod::Module, _path::String)  @ Base Base.jl:327  [13] top-level scope  @ ~/.julia/packages/XAM/gm2PK/src/XAM.jl:16  [14] include(mod::Module, _path::String)  @ Base Base.jl:326  [15] 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:3296  [16] top-level scope  @ stdin:5  [17] eval(m::Module, e::Any)  @ Core boot.jl:521  [18] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [19] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [20] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [21] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/sam/sam.jl:4 in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/XAM.jl:1 in expression starting at stdin:5 ✗ XAM ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("d759349c-bcba-11e9-07c2-5b90f8f05f7c"), "XAM") 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:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base 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_using(to::Module, path::Expr, flags::UInt8)  @ Base module.jl:137 [inlined]  [11] eval_using(to::Module, path::Expr)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:207  [12] top-level scope  @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/BioRecordsProcessing.jl:3  [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:3296  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core boot.jl:521  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [18] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [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/BioRecordsProcessing/Dw0CY/src/BioRecordsProcessing.jl:1 in expression starting at stdin:5 ✗ BioRecordsProcessing 19 dependencies successfully precompiled in 2323 seconds. 14 already precompiled. Precompilation completed after 2341.52s ################################################################################ # Loading # Loading BioRecordsProcessing... ┌ 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) (= #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 (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:3166  [2] 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:3736  [3] 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:4317  [4] 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:4133  [5] 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:1320  [6] 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:1270  [7] 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:4177  [8] 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:4133 [inlined]  [9] (::Base.JuliaLowering.var"#expand_forms_2##2#expand_forms_2##3"{Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}})(e::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4421 [inlined]  [10] 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  [11] 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:4421  [12] 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:4133 [inlined]  [13] 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:4450  [14] 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  [15] include(mapexpr::Function, mod::Module, _path::String)  @ Base Base.jl:327  [16] top-level scope  @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:93  [17] include(mod::Module, _path::String)  @ Base Base.jl:326  [18] 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:3296  [19] top-level scope  @ stdin:5  [20] eval(m::Module, e::Any)  @ Core boot.jl:521  [21] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [22] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [23] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [24] _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 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:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base loading.jl:2539 [inlined]  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)  @ Base module.jl:36 [inlined]  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)  @ Base module.jl:111  [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:195  [11] top-level scope  @ ~/.julia/packages/XAM/gm2PK/src/sam/sam.jl:8  [12] include(mapexpr::Function, mod::Module, _path::String)  @ Base Base.jl:327  [13] top-level scope  @ ~/.julia/packages/XAM/gm2PK/src/XAM.jl:16  [14] include(mod::Module, _path::String)  @ Base Base.jl:326  [15] 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:3296  [16] top-level scope  @ stdin:5  [17] eval(m::Module, e::Any)  @ Core boot.jl:521  [18] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [19] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [20] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [21] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/sam/sam.jl:4 in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/XAM.jl:1 in expression starting at stdin:5 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("d759349c-bcba-11e9-07c2-5b90f8f05f7c"), "XAM") 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:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base 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_using(to::Module, path::Expr, flags::UInt8)  @ Base module.jl:137 [inlined]  [11] eval_using(to::Module, path::Expr)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:207  [12] top-level scope  @ ~/.julia/packages/BioRecordsProcessing/Dw0CY/src/BioRecordsProcessing.jl:3  [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:3296  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core boot.jl:521  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [18] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [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/BioRecordsProcessing/Dw0CY/src/BioRecordsProcessing.jl:1 in expression starting at stdin:5 3 dependencies had output during precompilation: ┌ XAM │ 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:2837 │ [3] _require_prelocked(uuidkey::Base.PkgId, env::String) │ @ Base loading.jl:2685 │ [4] macro expansion │ @ loading.jl:2599 [inlined] │ [5] macro expansion │ @ lock.jl:376 [inlined] │ [6] __require(into::Module, mod::Symbol) │ @ Base loading.jl:2563 │ [7] require(into::Module, mod::Symbol) │ @ Base loading.jl:2539 [inlined] │ [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) │ @ Base module.jl:36 [inlined] │ [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr) │ @ Base module.jl:111 │ [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr) │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:195 │ [11] top-level scope │ @ ~/.julia/packages/XAM/gm2PK/src/sam/sam.jl:8 │ [12] include(mapexpr::Function, mod::Module, _path::String) │ @ Base Base.jl:327 │ [13] top-level scope │ @ ~/.julia/packages/XAM/gm2PK/src/XAM.jl:16 │ [14] include(mod::Module, _path::String) │ @ Base Base.jl:326 │ [15] 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:3296 │ [16] top-level scope │ @ stdin:5 │ [17] eval(m::Module, e::Any) │ @ Core boot.jl:521 │ [18] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) │ @ Base loading.jl:3132 │ [19] include_string(m::Module, txt::String, fname::String) │ @ Base loading.jl:3142 [inlined] │ [20] exec_options(opts::Base.JLOptions) │ @ Base client.jl:353 │ [21] _start() │ @ Base client.jl:596 │ in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/sam/sam.jl:4 │ in expression starting at /home/pkgeval/.julia/packages/XAM/gm2PK/src/XAM.jl:1 │ in expression starting at stdin:5 └ ┌ BioAlignments │ ┌ 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) (= #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 (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:3166 │ [2] 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:3736 │ [3] 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:4317 │ [4] 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:4133 │ [5] 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:1320 │ [6] 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:1270 │ [7] 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:4177 │ [8] 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:4133 [inlined] │ [9] (::Base.JuliaLowering.var"#expand_forms_2##2#expand_forms_2##3"{Base.JuliaLowering.DesugaringContext{Dict{Symbol, Dict{Int64, Any}}}})(e::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}) │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/desugaring.jl:4421 [inlined] │ [10] 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 │ [11] 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:4421 │ [12] 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:4133 [inlined] │ [13] 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:4450 │ [14] 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 │ [15] include(mapexpr::Function, mod::Module, _path::String) │ @ Base Base.jl:327 │ [16] top-level scope │ @ ~/.julia/packages/BioAlignments/I6ecx/src/BioAlignments.jl:93 │ [17] include(mod::Module, _path::String) │ @ Base Base.jl:326 │ [18] 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:3296 │ [19] top-level scope │ @ stdin:5 │ [20] eval(m::Module, e::Any) │ @ Core boot.jl:521 │ [21] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) │ @ Base loading.jl:3132 │ [22] include_string(m::Module, txt::String, fname::String) │ @ Base loading.jl:3142 [inlined] │ [23] exec_options(opts::Base.JLOptions) │ @ Base client.jl:353 │ [24] _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 └ ┌ BioRecordsProcessing │ [Output was shown above] └ ERROR: The following 3 packages failed to precompile: XAM Failed to precompile XAM [d759349c-bcba-11e9-07c2-5b90f8f05f7c] to "/home/pkgeval/.julia/compiled/v1.14/XAM/jl_WK2bAO" (ProcessExited(1)). BioAlignments Failed to precompile BioAlignments [00701ae9-d1dc-5365-b64a-a3a3ebf5695e] to "/home/pkgeval/.julia/compiled/v1.14/BioAlignments/jl_4lhd9G" (ProcessExited(1)). BioRecordsProcessing Failed to precompile BioRecordsProcessing [321bc2d7-9525-42af-8b23-17b2621d5ea8] to "/home/pkgeval/.julia/compiled/v1.14/BioRecordsProcessing/jl_kGvurR" (ProcessExited(1)). Loading failed after 165.68s ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --check-bounds=yes --pkgimages=existing -e 'using BioRecordsProcessing'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error(proc::Base.Process) @ Base process.jl:612 [inlined] [2] run(::Cmd; wait::Bool) @ Base process.jl:525 [3] run(::Cmd) @ Base process.jl:522 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:197 [5] include(mod::Module, _path::String) @ Base Base.jl:326 [6] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [7] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:188 PkgEval failed after 2546.17s: package fails to precompile