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RData can't load .rda files with FileIO@1.10.0 but can with FileIO@1.9.0 #89

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jonasjonker opened this issue Jun 21, 2021 · 3 comments
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RData can't load .rda files with FileIO@1.10.0 but can with FileIO@1.9.0 #89

jonasjonker opened this issue Jun 21, 2021 · 3 comments

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@jonasjonker
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FileIO@1.10.0 causes RData to throw a load error which can be solved by downgrading to FileIO@1.9.0.

 pkg> status
      Status `~/Repos/juliaplotting/Project.toml`
  [5789e2e9] FileIO v1.10.0
  [91a5bcdd] Plots v1.16.5
  [c3e4b0f8] Pluto v0.14.8
  [ce6b1742] RDatasets v0.7.5
julia> using RDatasets
julia> iris = dataset("datasets", "iris")
Error encountered while load FileIO.File{FileIO.DataFormat{:RData}, String}("/home/jonas/.julia/packages/RDatasets/eRbZP/src/../data/datasets/iris.rda").

Fatal error:
ERROR: RData load error: neither load nor fileio_load is defined
  due to MethodError(seek, (TranscodingStreams.TranscodingStream{CodecZlib.GzipDecompressor, IOStream}(<mode=close>), 0), 0x00000000000073cb)
  Will try next loader.

Stacktrace:
  [1] getlength(io::TranscodingStreams.TranscodingStream{CodecZlib.GzipDecompressor, IOStream}, pos::Int64)
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/query.jl:62
  [2] getlength(io::TranscodingStreams.TranscodingStream{CodecZlib.GzipDecompressor, IOStream})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/query.jl:60
  [3] detect_rdata(io::TranscodingStreams.TranscodingStream{CodecZlib.GzipDecompressor, IOStream})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/registry.jl:62
  [4] fileio_load(s::FileIO.Stream{FileIO.DataFormat{:RData}, TranscodingStreams.TranscodingStream{CodecZlib.GzipDecompressor, IOStream}, String}; kwoptions::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ RData ~/.julia/packages/RData/Re6gn/src/RData.jl:53
  [5] fileio_load(s::FileIO.Stream{FileIO.DataFormat{:RData}, TranscodingStreams.TranscodingStream{CodecZlib.GzipDecompressor, IOStream}, String})
    @ RData ~/.julia/packages/RData/Re6gn/src/RData.jl:52
  [6] fileio_load(f::FileIO.File{FileIO.DataFormat{:RData}, String}; kwoptions::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ RData ~/.julia/packages/RData/Re6gn/src/RData.jl:95
  [7] fileio_load(f::FileIO.File{FileIO.DataFormat{:RData}, String})
    @ RData ~/.julia/packages/RData/Re6gn/src/RData.jl:92
  [8] #invokelatest#2
    @ ./essentials.jl:708 [inlined]
  [9] invokelatest
    @ ./essentials.jl:706 [inlined]
 [10] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:217
 [11] action
    @ ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:197 [inlined]
 [12] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Symbol, ::String; options::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:185
 [13] action
    @ ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:185 [inlined]
 [14] load(::String; options::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:113
 [15] load
    @ ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:110 [inlined]
 [16] dataset(package_name::String, dataset_name::String)
    @ RDatasets ~/.julia/packages/RDatasets/eRbZP/src/dataset.jl:12
 [17] top-level scope
    @ REPL[2]:1
 [18] eval
    @ ./boot.jl:360 [inlined]
 [19] eval_user_input(ast::Any, backend::REPL.REPLBackend)
    @ REPL /opt/julia/usr/share/julia/stdlib/v1.6/REPL/src/REPL.jl:139
 [20] repl_backend_loop(backend::REPL.REPLBackend)
    @ REPL /opt/julia/usr/share/julia/stdlib/v1.6/REPL/src/REPL.jl:200
 [21] start_repl_backend(backend::REPL.REPLBackend, consumer::Any)
    @ REPL /opt/julia/usr/share/julia/stdlib/v1.6/REPL/src/REPL.jl:185
 [22] run_repl(repl::REPL.AbstractREPL, consumer::Any; backend_on_current_task::Bool)
    @ REPL /opt/julia/usr/share/julia/stdlib/v1.6/REPL/src/REPL.jl:317
 [23] run_repl(repl::REPL.AbstractREPL, consumer::Any)
    @ REPL /opt/julia/usr/share/julia/stdlib/v1.6/REPL/src/REPL.jl:305
 [24] (::Base.var"#874#876"{Bool, Bool, Bool})(REPL::Module)
    @ Base ./client.jl:387
 [25] #invokelatest#2
    @ ./essentials.jl:708 [inlined]
 [26] invokelatest
    @ ./essentials.jl:706 [inlined]
 [27] run_main_repl(interactive::Bool, quiet::Bool, banner::Bool, history_file::Bool, color_set::Bool)
    @ Base ./client.jl:372
 [28] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:302
 [29] _start()
    @ Base ./client.jl:485
Stacktrace:
  [1] handle_error(e::FileIO.LoaderError, q::Base.PkgId, bt::Vector{Union{Ptr{Nothing}, Base.InterpreterIP}})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/error_handling.jl:61
  [2] handle_exceptions(exceptions::Vector{Tuple{Any, Union{Base.PkgId, Module}, Vector{T} where T}}, action::String)
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/error_handling.jl:56
  [3] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::FileIO.Formatted; options::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:226
  [4] action
    @ ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:197 [inlined]
  [5] action(::Symbol, ::Vector{Union{Base.PkgId, Module}}, ::Symbol, ::String; options::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:185
  [6] action
    @ ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:185 [inlined]
  [7] load(::String; options::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ FileIO ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:113
  [8] load
    @ ~/.julia/packages/FileIO/LoVdY/src/loadsave.jl:110 [inlined]
  [9] dataset(package_name::String, dataset_name::String)
    @ RDatasets ~/.julia/packages/RDatasets/eRbZP/src/dataset.jl:12
 [10] top-level scope
    @ REPL[2]:1

 pkg> add FileIO@1.9.0
... 

julia> iris = dataset("datasets", "iris")
150×5 DataFrame
 Row │ SepalLength  SepalWidth  PetalLength  PetalWidth  Species   
     │ Float64      Float64     Float64      Float64     Cat…      
─────┼─────────────────────────────────────────────────────────────
   1 │         5.1         3.5          1.4         0.2  setosa
   2 │         4.9         3.0          1.4         0.2  setosa
  ⋮  │      ⋮           ⋮            ⋮           ⋮           ⋮
 149 │         6.2         3.4          5.4         2.3  virginica
 150 │         5.9         3.0          5.1         1.8  virginica
                                                   146 rows omitted
@alyst
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alyst commented Jun 21, 2021

Thanks for reporting! I can reproduce it with ]test RData.
To me it looks like the issue could be caused by the changes in package loading logic in FileIO 1.10, in particular related to this commit.
Could you please submit a bug report there (referencing this issue)?

@jonasjonker jonasjonker mentioned this issue Jun 21, 2021
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@jonasjonker
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Yes I can. You can find it here.

@alyst
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alyst commented Jun 21, 2021

fixed upstream (FileIO v1.10.1)

@alyst alyst closed this as completed Jun 21, 2021
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@alyst @jonasjonker