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failed to run `@example` block in src/examples.md:30-37 ```@example examples corr_response, corr_MID, mean_enrichment, residuum = isotope_correction(response_vec, ala_m57; tracer_purity = 0.8) @test corr_response ≈ [3.7494356377578774e6, 1.582246275076472e6, 3.110758584864337e6, 392021.5450371306] @test corr_MID ≈ [0.42441018135800024, 0.17909933478943207, 0.3521163563572243, 0.04437412749534335] @test mean_enrichment ≈ 0.5041136074974777 @test isapprox(residuum, [7.161631798132872e-13, 8.285188904175392e-13, -1.0657673462843284e-12, 6.363440591555375e-13]; atol = 1e16) ``` exception = LoadError: UndefVarError: `@test` not defined Stacktrace: [1] top-level scope @ :0 [2] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [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 examples.md:33

failed to run `@example` block in src/examples.md:42-47 ```@example examples corr_response, corr_MID, mean_enrichment = isotope_correction(response_vec, pyruvate; tracer_purity = 0.8, optimization = false) @test corr_response ≈ [2.788815753935856e6, 1.7402842780064365e6, 2.8703208164970432e6, 961526.0409580052] @test corr_MID ≈ [0.333552621590313, 0.20814440051201863, 0.3433009268527882, 0.11500205104488019] @test mean_enrichment ≈ 0.5599381018380588 ``` exception = UndefVarError: `pyruvate` not defined Stacktrace: [1] top-level scope @ examples.md:43 [2] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [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/examples.md:52-72 ```@example examples using ColorSchemes, CairoMakie colors = colorschemes[:bamako][1:64:end]; group_color = [PolyElement(color = color, strokecolor = :transparent) for color in colors] labels = ["m+0", "m+1", "m+2", "m+3"] Mplus = [0, 1, 2, 3] fig = Figure(); ax = Axis(fig[1,1], xticks = (1:2, ["uncorrected", "corrected"]), title = "Alanine (M-57) MID") barplot!(ax, repeat([1, 2], inner = length(corr_MID)), cat(MID, corr_MID, dims = 1), stack = repeat(Mplus, 2), colormap = colors, color = repeat(Mplus .+ 1, 2)) Legend(fig[1,2], group_color, labels, framevisible = false) fig ``` exception = ArgumentError: Package ColorSchemes not found in current path. - Run `import Pkg; Pkg.add("ColorSchemes")` to install the ColorSchemes package. Stacktrace: [1] macro expansion @ ./loading.jl:1772 [inlined] [2] macro expansion @ ./lock.jl:267 [inlined] [3] __require(into::Module, mod::Symbol) @ Base ./loading.jl:1753 [4] #invoke_in_world#3 @ ./essentials.jl:926 [inlined] [5] invoke_in_world @ ./essentials.jl:923 [inlined] [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:1746 [7] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [13] with_logger @ ./logging.jl:627 [inlined] [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/examples.md:76-78 ```@example examples using CSV, DataFrames, DataFramesMeta ``` exception = ArgumentError: Package CSV not found in current path. - Run `import Pkg; Pkg.add("CSV")` to install the CSV package. Stacktrace: [1] macro expansion @ ./loading.jl:1772 [inlined] [2] macro expansion @ ./lock.jl:267 [inlined] [3] __require(into::Module, mod::Symbol) @ Base ./loading.jl:1753 [4] #invoke_in_world#3 @ ./essentials.jl:926 [inlined] [5] invoke_in_world @ ./essentials.jl:923 [inlined] [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:1746 [7] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [13] with_logger @ ./logging.jl:627 [inlined] [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/examples.md:90-99 ```@example examples df = DataFrame( Sample = repeat([1, 2], inner = 11), AminoAcidFragment = repeat(cat(repeat(["Met_(M-159)"], 5), repeat(["Met_(M-57)"], 6), dims = 1), 2), Molecule = repeat(cat(repeat(["C10H24N1S1Si1LabC4"], 5), repeat(["C13H30N1O2S1Si2LabC5"], 6), dims = 1), 2), MZ0 = repeat(cat(repeat([218], 5), repeat([320], 6), dims = 1), 2), Mplus = repeat(cat(repeat(0:4, 1), repeat(0:5, 1), dims = 1), 2), Response = cat(repeat([1e6/5], 5), repeat([1e6/6], 6), rand(0:1e6, 11), dims = 1) ) ``` exception = UndefVarError: `DataFrame` not defined Stacktrace: [1] top-level scope @ examples.md:91 [2] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [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/examples.md:112-117 ```@example examples gdfs = groupby(df, [:Sample, :AminoAcidFragment]) df_corrected = @Transform(gdfs, :CorrectedResponse = isotope_correction(Vector(:Response), :Molecule[1]; tracer_purity = 0.99)[1] ) ``` exception = UndefVarError: `df` not defined Stacktrace: [1] top-level scope @ examples.md:113 [2] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [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/examples.md:121-138 ```@example examples gdfs_corrected = groupby(df_corrected, [:Sample, :AminoAcidFragment]) df_corrected_MIDs = @Transform(gdfs_corrected, :MID = :Response ./ sum(:Response), :CorrectedMID = :CorrectedResponse ./ sum(:CorrectedResponse) ) @test df_corrected_MIDs.CorrectedResponse[1:11] ≈ [256350.5953947725, 209316.21271342717, 213614.23098928804, 213323.38585836615, 215543.78052654164, 240727.618300901, 176403.71542171348, 168185.8260919769, 173128.23316293195, 173266.76220269877, 174721.82172768374 ] @test df_corrected_MIDs.CorrectedMID[1:11] ≈ [0.2313324103459418, 0.18888828378538802, 0.19276684285771886, 0.19250438235876846, 0.19450808065218303, 0.21757070311023, 0.15943447065382058, 0.1520071053511907, 0.15647407507022204, 0.1565992782388322, 0.15791436757570465 ] ``` exception = UndefVarError: `df_corrected` not defined Stacktrace: [1] top-level scope @ examples.md:122 [2] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [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/examples.md:142-144 ```@example examples CSV.write("Corrected_MIDs.csv", df_corrected_MIDs) ``` exception = UndefVarError: `CSV` not defined Stacktrace: [1] top-level scope @ examples.md:143 [2] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [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/examples.md:148-181 ```@example examples using ColorSchemes, CairoMakie gdfs = @groupby(df_corrected_MIDs, :Sample, :AminoAcidFragment) colors = colorschemes[:bamako][1:43:256]; group_color = [PolyElement(color = color, strokecolor = :transparent) for color in colors] labels = ["m+0", "m+1", "m+2", "m+3", "m+4", "m+5"] fig = Figure(); function myplot(group, fig, colors) name = group.AminoAcidFragment[1] sample = group.Sample[1] ax = Axis(fig, xticks = (1:2, ["uncorrected", "corrected"]), title = "Sample $sample $name MID") barplot!(ax, repeat([1, 2], inner = length(group.MID)), cat(group.MID, group.CorrectedMID, dims = 1), stack = repeat(group.Mplus, 2), colormap = colors, color = repeat(group.Mplus .+ 1, 2)) end myplot(gdfs[1], fig[1,1], colors[1:5]) myplot(gdfs[2], fig[1,2], colors) myplot(gdfs[3], fig[2,1], colors[1:5]) myplot(gdfs[4], fig[2,2], colors) Legend(fig[1:2,3], group_color, labels, framevisible = false) fig #save("Methionine_MIDs.png", fig) ``` exception = ArgumentError: Package ColorSchemes not found in current path. - Run `import Pkg; Pkg.add("ColorSchemes")` to install the ColorSchemes package. Stacktrace: [1] macro expansion @ ./loading.jl:1772 [inlined] [2] macro expansion @ ./lock.jl:267 [inlined] [3] __require(into::Module, mod::Symbol) @ Base ./loading.jl:1753 [4] #invoke_in_world#3 @ ./essentials.jl:926 [inlined] [5] invoke_in_world @ ./essentials.jl:923 [inlined] [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:1746 [7] eval @ ./boot.jl:385 [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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [13] with_logger @ ./logging.jl:627 [inlined] [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