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RData can't load .rda files with FileIO@1.10.0 but can with FileIO@1.9.0 #345

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jonasjonker opened this issue Jun 21, 2021 · 2 comments · Fixed by #346
Closed

RData can't load .rda files with FileIO@1.10.0 but can with FileIO@1.9.0 #345

jonasjonker opened this issue Jun 21, 2021 · 2 comments · Fixed by #346

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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
@jonasjonker
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I raised this issue as well at RData.jl

@johnnychen94
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A PR's coming.

@jonasjonker jonasjonker mentioned this issue Jun 21, 2021
Closed
@johnnychen94 johnnychen94 mentioned this issue Jun 21, 2021
Merged
@devmotion devmotion mentioned this issue Aug 22, 2021
Merged
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check eof before read bytes JuliaIO/FileIO.jl
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@johnnychen94 @jonasjonker