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safer indexing for AbstractArray #339

safer indexing for AbstractArray

safer indexing for AbstractArray #339

Triggered via pull request July 22, 2024 16:44
@paldaypalday
synchronize #540
pa/eachindex
Status Failure
Total duration 5m 25s
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5 errors and 1 notice
build: ../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/conversions.md:66-70 ```@example 1 # julia -> R d = DateTime(2012, 12, 12, 12, 12, 12) r = robject(d) ``` exception = MethodError: no method matching keys(::Ptr{StrSxp}) Closest candidates are: keys(!Matched::IndexLinear, !Matched::DataFrames.GroupedDataFrame) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/groupeddataframe.jl:574 keys(!Matched::Pkg.Registry.RegistryInstance) @ Pkg /usr/local/julia1.10.4/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:447 keys(!Matched::Pkg.Types.Manifest) @ Pkg /usr/local/julia1.10.4/share/julia/stdlib/v1.10/Pkg/src/Types.jl:318 ... Stacktrace: [1] eachindex(itrs::Ptr{StrSxp}) @ Base ./abstractarray.jl:318 [2] sexp(::Type{RCall.RClass{:character}}, a::Vector{String}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/base.jl:269 [3] sexp(s::Vector{String}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:214 [4] sexp(::Type{RCall.RClass{:POSIXct}}, d::Dates.DateTime) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/datetime.jl:83 [5] sexp(s::Dates.DateTime) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:214 [6] RObject(s::Dates.DateTime) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:209 [7] robject(s::Dates.DateTime) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:208 [8] top-level scope @ conversions.md:69 [9] eval @ ./boot.jl:385 [inlined] [10] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [11] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [12] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [13] (::IOCapture.var"#5#9"{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/Y5rEA/src/IOCapture.jl:170 [14] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [15] with_logger @ ./logging.jl:627 [inlined] [16] capture(f::Documenter.var"#57#59"{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 [17] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
build: ../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/conversions.md:93-97 ```@example 1 d = DataFrame([[1.0, 4.5, 7.0]], [:x]) # Julia -> R r = robject(d) ``` exception = MethodError: no method matching keys(::Ptr{StrSxp}) Closest candidates are: keys(!Matched::IndexLinear, !Matched::DataFrames.GroupedDataFrame) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/groupeddataframe.jl:574 keys(!Matched::Pkg.Registry.RegistryInstance) @ Pkg /usr/local/julia1.10.4/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:447 keys(!Matched::Pkg.Types.Manifest) @ Pkg /usr/local/julia1.10.4/share/julia/stdlib/v1.10/Pkg/src/Types.jl:318 ... Stacktrace: [1] eachindex(itrs::Ptr{StrSxp}) @ Base ./abstractarray.jl:318 [2] sexp(::Type{RCall.RClass{:character}}, a::Vector{String}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/base.jl:269 [3] sexp(s::Vector{String}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:214 [4] setattrib!(s::Ptr{VecSxp}, sym::RObject{RCall.SymSxp}, t::Vector{String}) @ RCall ~/work/RCall.jl/RCall.jl/src/methods.jl:347 [5] sexp(::Type{RCall.RClass{:list}}, d::DataFrames.DataFrame) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/dataframe.jl:27 [6] sexp(s::DataFrames.DataFrame) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:214 [7] RObject(s::DataFrames.DataFrame) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:209 [8] robject(s::DataFrames.DataFrame) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:208 [9] top-level scope @ conversions.md:96 [10] eval @ ./boot.jl:385 [inlined] [11] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [12] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [13] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [14] (::IOCapture.var"#5#9"{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/Y5rEA/src/IOCapture.jl:170 [15] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [16] with_logger @ ./logging.jl:627 [inlined] [17] capture(f::Documenter.var"#57#59"{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 [18] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
build: ../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/conversions.md:118-122 ```@example 1 # Julia -> R aa = AxisArray([1,2,3], Axis{:id}(["a", "b", "c"])) r = robject(aa) ``` exception = MethodError: no method matching keys(::Ptr{StrSxp}) Closest candidates are: keys(!Matched::IndexLinear, !Matched::DataFrames.GroupedDataFrame) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/groupeddataframe/groupeddataframe.jl:574 keys(!Matched::Pkg.Registry.RegistryInstance) @ Pkg /usr/local/julia1.10.4/share/julia/stdlib/v1.10/Pkg/src/Registry/registry_instance.jl:447 keys(!Matched::Pkg.Types.Manifest) @ Pkg /usr/local/julia1.10.4/share/julia/stdlib/v1.10/Pkg/src/Types.jl:318 ... Stacktrace: [1] eachindex(itrs::Ptr{StrSxp}) @ Base ./abstractarray.jl:318 [2] sexp(::Type{RCall.RClass{:character}}, a::Vector{String}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/base.jl:269 [3] sexp(s::Vector{String}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:214 [4] setindex!(s::Ptr{VecSxp}, value::Vector{String}, key::Int64) @ RCall ~/work/RCall.jl/RCall.jl/src/methods.jl:195 [5] sexp(::Type{RCall.RClass{:list}}, d::OrderedCollections.OrderedDict{Symbol, Vector{String}}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/base.jl:288 [6] sexp @ ~/work/RCall.jl/RCall.jl/src/convert/default.jl:214 [inlined] [7] setattrib! @ ~/work/RCall.jl/RCall.jl/src/methods.jl:347 [inlined] [8] sexp(::Type{RCall.RClass{:array}}, aa::AxisArrays.AxisVector{Int64, Vector{Int64}, Tuple{AxisArrays.Axis{:id, Vector{String}}}}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/axisarray.jl:25 [9] sexp @ ~/work/RCall.jl/RCall.jl/src/convert/default.jl:214 [inlined] [10] RObject @ ~/work/RCall.jl/RCall.jl/src/convert/default.jl:209 [inlined] [11] robject(s::AxisArrays.AxisVector{Int64, Vector{Int64}, Tuple{AxisArrays.Axis{:id, Vector{String}}}}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/default.jl:208 [12] top-level scope @ conversions.md:121 [13] eval @ ./boot.jl:385 [inlined] [14] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [15] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [16] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [17] (::IOCapture.var"#5#9"{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/Y5rEA/src/IOCapture.jl:170 [18] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [19] with_logger @ ./logging.jl:627 [inlined] [20] capture(f::Documenter.var"#57#59"{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 [21] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:752
build: ../../../.julia/packages/Documenter/qoyeC/src/utilities/utilities.jl#L44
failed to run `@example` block in src/conversions.md:124-127 ```@example 1 # R -> Julia rcopy(AxisArray, r) ``` exception = r has no dimnames Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] rcopy(::Type{AxisArrays.AxisArray}, r::Ptr{RealSxp}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/axisarray.jl:5 [3] rcopy(::Type{AxisArrays.AxisArray}, r::RObject{RealSxp}) @ RCall ~/work/RCall.jl/RCall.jl/src/convert/base.jl:18 [4] top-level scope @ conversions.md:126 [5] eval @ ./boot.jl:385 [inlined] [6] #58 @ ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:754 [inlined] [7] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [8] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/qoyeC/src/expander_pipeline.jl:753 [9] (::IOCapture.var"#5#9"{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/Y5rEA/src/IOCapture.jl:170 [10] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [11] with_logger @ ./logging.jl:627 [inlined] [12] capture(f::Documenter.var"#57#59"{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/qoyeC/src/expander_pipeline.jl:752
build
Process completed with exit code 1.
[julia-buildpkg] Caching of the julia depot was not detected
Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`