failed to run `@example` block in src/man/bootstrap.md:56-59 ```@example bootstrap bootnet = readMultiTopology(joinpath(dirname(pathof(SNaQ)), "..","examples","bootsnaq.out")); length(bootnet) ``` exception = SystemError: opening file "/home/runner/work/SNaQ.jl/SNaQ.jl/src/../examples/bootsnaq.out": No such file or directory Stacktrace: [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) @ Base ./error.jl:176 [2] systemerror @ ./error.jl:175 [inlined] [3] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) @ Base ./iostream.jl:295 [4] open @ ./iostream.jl:277 [inlined] [5] open(f::Base.var"#494#495"{@kwargs{}}, args::String; kwargs::@kwargs{}) @ Base ./io.jl:408 [6] open @ ./io.jl:407 [inlined] [7] #readlines#493 @ ./io.jl:704 [inlined] [8] readlines @ ./io.jl:703 [inlined] [9] readMultiTopology(file::String, fast::Bool) @ PhyloNetworks ~/.julia/packages/PhyloNetworks/ZTcKe/src/readwrite.jl:882 [10] readMultiTopology(file::String) @ PhyloNetworks ~/.julia/packages/PhyloNetworks/ZTcKe/src/readwrite.jl:881 [11] top-level scope @ bootstrap.md:57 [12] eval @ ./boot.jl:430 [inlined] [13] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [14] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [15] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [16] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [17] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [18] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [19] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [20] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/bootstrap.md:74-76 ```@example bootstrap net1 = readTopology(joinpath(dirname(pathof(SNaQ)), "..","examples","net1.out")) ``` exception = Could not find or open /home/runner/work/SNaQ.jl/SNaQ.jl/src/../examples/net1.out file Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] readTopology(input::String, verbose::Bool) @ PhyloNetworks ~/.julia/packages/PhyloNetworks/ZTcKe/src/readwrite.jl:492 [3] readTopology(input::String) @ PhyloNetworks ~/.julia/packages/PhyloNetworks/ZTcKe/src/readwrite.jl:518 [4] top-level scope @ bootstrap.md:75 [5] eval @ ./boot.jl:430 [inlined] [6] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [7] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [8] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [9] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [10] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [11] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [12] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [13] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752

failed to run `@setup` block in src/man/bootstrap.md ```@setup bootstrap rootonedge!(net1, 7) ``` exception = LoadError: UndefVarError: `net1` not defined in `Main.__atexample__named__bootstrap` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ string:1 [2] eval @ ./boot.jl:430 [inlined] [3] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2643 [4] include_string (repeats 2 times) @ ./loading.jl:2653 [inlined] [5] #67 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:907 [inlined] [6] cd(f::Documenter.var"#67#68"{Module, MarkdownAST.CodeBlock}, dir::String) @ Base.Filesystem ./file.jl:112 [7] runner(::Type{Documenter.Expanders.SetupBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:906 in expression starting at string:1

failed to run `@example` block in src/man/bootstrap.md:86-99 ```@example bootstrap using PhyloPlots, RCall R"name <- function(x) file.path('..', 'assets', 'figures', x)" # hide R"svg(name('net1_rotate1_1.svg'), width=4, height=4)" # hide R"par"(mar=[0,0,0,0]) # hide plot(net1, showedgenumber=true); # edge 7 leads to O+E R"dev.off()" # hide rootonedge!(net1, 7) # makes (O,E) outgroup clade R"svg(name('net1_rotate1_2.svg'), width=4, height=4)" # hide R"par"(mar=[0,0,0,0]) # hide plot(net1, shownodenumber=true); R"dev.off()" # hide nothing # hide ``` exception = ArgumentError: Package PhyloPlots not found in current path. - Run `import Pkg; Pkg.add("PhyloPlots")` to install the PhyloPlots package. Stacktrace: [1] macro expansion @ ./loading.jl:2223 [inlined] [2] macro expansion @ ./lock.jl:273 [inlined] [3] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2198 [4] #invoke_in_world#3 @ ./essentials.jl:1089 [inlined] [5] invoke_in_world @ ./essentials.jl:1086 [inlined] [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:2191 [7] eval @ ./boot.jl:430 [inlined] [8] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [9] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [10] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [11] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [12] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [13] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [14] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [15] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/bootstrap.md:105-107 ```@example bootstrap rotate!(net1, -6) ``` exception = UndefVarError: `net1` not defined in `Main.__atexample__named__bootstrap` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ bootstrap.md:106 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/bootstrap.md:108-114 ```@example bootstrap R"svg(name('net1_rotate2.svg'), width=4, height=4)" # hide R"par"(mar=[0,0,0,0]) # hide plot(net1, showgamma=true); R"dev.off()" # hide nothing # hide ``` exception = LoadError: UndefVarError: `@R_str` not defined in `Main.__atexample__named__bootstrap` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ :0 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752 in expression starting at bootstrap.md:109

failed to run `@example` block in src/man/bootstrap.md:121-123 ```@example bootstrap BSe_tree, tree1 = treeEdgesBootstrap(bootnet,net1); ``` exception = UndefVarError: `treeEdgesBootstrap` not defined in `Main.__atexample__named__bootstrap` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ bootstrap.md:122 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752

failed to run `@example` block in src/man/bootstrap.md:127-133 ```@example bootstrap R"svg(name('major_tree.svg'), width=4, height=4)" # hide R"par"(mar=[0,0,0,0]) # hide plot(tree1, showedgenumber=true); R"dev.off()" # hide nothing # hide ``` exception = LoadError: UndefVarError: `@R_str` not defined in `Main.__atexample__named__bootstrap` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ :0 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752 in expression starting at bootstrap.md:128

failed to run `@example` block in src/man/bootstrap.md:150-160 ```@example bootstrap R"svg(name('boot_tree_net_1.svg'), width=4, height=4)" # hide R"par"(mar=[0,0,0,0]) # hide plot(tree1, edgelabel=BSe_tree); R"dev.off()" # hide R"svg(name('boot_tree_net_2.svg'), width=4, height=4)" # hide R"par"(mar=[0,0,0,0]) # hide plot(net1, edgelabel=BSe_tree); R"dev.off()" # hide nothing # hide ``` exception = LoadError: UndefVarError: `@R_str` not defined in `Main.__atexample__named__bootstrap` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ :0 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752 in expression starting at bootstrap.md:151