Process completed with exit code 1.

Process completed with exit code 1.

failed to run `@example` block in src/benches.md:9-26 ```@example 1 using RCall using NetSurvival, RateTables, BenchmarkTools R_bench = @benchmark R""" relsurv::rs.surv( survival::Surv(time, stat) ~1, rmap=list(age = age, sex = sex, year = diag), data = relsurv::colrec, ratetable = relsurv::slopop, method = "pohar-perme", add.times=1:8149) """ jl_bench = @benchmark fit(PoharPerme, @formula(Surv(time,status)~1), colrec, slopop) ratio = time(minimum(R_bench)) / time(minimum(jl_bench)) ``` exception = UndefVarError: `_get_rate_predictors` not defined Stacktrace: [1] fit(::Type{PoharPerme}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.ConstantTerm{Int64}}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:34 [2] var"##core#229"() @ Main.__atexample__named__1 ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:561 [3] var"##sample#230"(::Tuple{}, __params::BenchmarkTools.Parameters) @ Main.__atexample__named__1 ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:570 [4] _lineartrial(b::BenchmarkTools.Benchmark, p::BenchmarkTools.Parameters; maxevals::Int64, kwargs::@kwargs{}) @ BenchmarkTools ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:187 [5] _lineartrial(b::BenchmarkTools.Benchmark, p::BenchmarkTools.Parameters) @ BenchmarkTools ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:182 [6] #invokelatest#2 @ ./essentials.jl:892 [inlined] [7] invokelatest @ ./essentials.jl:889 [inlined] [8] #lineartrial#46 @ ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:51 [inlined] [9] lineartrial @ ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:50 [inlined] [10] tune!(b::BenchmarkTools.Benchmark, p::BenchmarkTools.Parameters; progressid::Nothing, nleaves::Float64, ndone::Float64, verbose::Bool, pad::String, kwargs::@kwargs{}) @ BenchmarkTools ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:300 [11] tune! @ ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:289 [inlined] [12] tune!(b::BenchmarkTools.Benchmark) @ BenchmarkTools ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:289 [13] top-level scope @ ~/.julia/packages/BenchmarkTools/QNsku/src/execution.jl:447 [14] eval @ ./boot.jl:385 [inlined] [15] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [16] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [17] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [18] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [19] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [20] with_logger @ ./logging.jl:627 [inlined] [21] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [22] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:115-117 ```@example 2 e1 = fit(EdererI, @formula(Surv(time5,status5)~1), colrec, slopop) ``` exception = UndefVarError: `_get_rate_predictors` not defined Stacktrace: [1] fit(::Type{EdererI}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.ConstantTerm{Int64}}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:34 [2] top-level scope @ example.md:116 [3] eval @ ./boot.jl:385 [inlined] [4] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [5] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [6] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [7] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [8] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [9] with_logger @ ./logging.jl:627 [inlined] [10] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:121-124 ```@example 2 crude_e1 = CrudeMortality(e1) println(crude_e1.Λₒ[1826], " , ", crude_e1.Λₑ[1826], " , ", crude_e1.Λₚ[1826]) ``` exception = UndefVarError: `e1` not defined Stacktrace: [1] top-level scope @ example.md:122 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:129-131 ```@example 2 e2 = fit(EdererII, @formula(Surv(time5,status5)~1), colrec, slopop) ``` exception = UndefVarError: `_get_rate_predictors` not defined Stacktrace: [1] fit(::Type{EdererII}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.ConstantTerm{Int64}}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:34 [2] top-level scope @ example.md:130 [3] eval @ ./boot.jl:385 [inlined] [4] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [5] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [6] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [7] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [8] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [9] with_logger @ ./logging.jl:627 [inlined] [10] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:135-138 ```@example 2 crude_e2 = CrudeMortality(e2) println(crude_e2.Λₒ[1826], " , ", crude_e2.Λₑ[1826], " , ", crude_e2.Λₚ[1826]) ``` exception = UndefVarError: `e2` not defined Stacktrace: [1] top-level scope @ example.md:136 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:142-144 ```@example 2 pp = fit(PoharPerme, @formula(Surv(time5,status5)~1), colrec, slopop) ``` exception = UndefVarError: `_get_rate_predictors` not defined Stacktrace: [1] fit(::Type{PoharPerme}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.ConstantTerm{Int64}}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:34 [2] top-level scope @ example.md:143 [3] eval @ ./boot.jl:385 [inlined] [4] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [5] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [6] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [7] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [8] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [9] with_logger @ ./logging.jl:627 [inlined] [10] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:148-151 ```@example 2 crude_pp = CrudeMortality(pp) println(crude_pp.Λₒ[1826], " , ", crude_pp.Λₑ[1826], " , ", crude_pp.Λₚ[1826]) ``` exception = UndefVarError: `pp` not defined Stacktrace: [1] top-level scope @ example.md:149 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:157-168 ```@example 2 conf_int = confint(pp; level = 0.05) lower_bounds = [lower[1] for lower in conf_int] upper_bounds = [upper[2] for upper in conf_int] p1 = plot(pp.grid, pp.Sₑ, ribbon=(pp.Sₑ - lower_bounds, upper_bounds - pp.Sₑ), xlab = "Time (days)", ylab = "Net survival", label = false) p2 = plot(pp.grid, crude_pp.Λₑ, label = "Excess Mortality Rate") p2 = plot!(pp.grid, crude_pp.Λₚ, label = "Population Mortality Rate") plot(p1,p2) ``` exception = UndefVarError: `pp` not defined Stacktrace: [1] top-level scope @ example.md:158 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/example.md:176-178 ```@example 2 pp_sex = fit(PoharPerme, @formula(Surv(time5,status5)~sex), colrec, slopop) ``` exception = UndefVarError: `_get_rate_predictors` not defined Stacktrace: [1] fit(::Type{PoharPerme}, formula::StatsModels.FormulaTerm{StatsModels.FunctionTerm{typeof(Surv), Vector{StatsModels.Term}}, StatsModels.Term}, df::DataFrames.DataFrame, rt::RateTables.RateTable{1, @NamedTuple{sex::Tuple{Symbol, Symbol}}, @NamedTuple{female::RateTables.BasicRateTable, male::RateTables.BasicRateTable}}) @ NetSurvival ~/work/NetSurvival.jl/NetSurvival.jl/src/NPNSEstimator.jl:34 [2] top-level scope @ example.md:177 [3] eval @ ./boot.jl:385 [inlined] [4] #58 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:754 [inlined] [5] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [6] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:753 [7] (::IOCapture.var"#4#7"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:161 [8] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [9] with_logger @ ./logging.jl:627 [inlined] [10] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [11] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752