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No method matching isfinite for nullable Int64 #1083

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alexomics opened this issue Jan 2, 2018 · 8 comments
Closed

No method matching isfinite for nullable Int64 #1083

alexomics opened this issue Jan 2, 2018 · 8 comments

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@alexomics
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julia> versioninfo()
Julia Version 0.6.2
Commit d386e40c17 (2017-12-13 18:08 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin14.5.0)
  CPU: Intel(R) Core(TM) i5-2415M CPU @ 2.30GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Sandybridge)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, sandybridge)

julia> Pkg.status("Gadfly")
 - Gadfly                        0.6.4

julia> head(s)
6×2 DataFrames.DataFrame
│ Row │ foo │ bar     │
├─────┼─────┼─────────┤
│ 1   │ 521 │ 40.0    │
│ 2   │ 521 │ 40.0003 │
│ 3   │ 542 │ 40.0005 │
│ 4   │ 540 │ 40.0007 │
│ 5   │ 566 │ 40.001  │
│ 6   │ 664 │ 40.0012 │

julia> plot(s, x="bar", y="foo", Geom.line)
Error showing value of type Gadfly.Plot:
ERROR: MethodError: no method matching isfinite(::Nullable{Int64})
Closest candidates are:
  isfinite(::Float16) at float.jl:539
  isfinite(::BigFloat) at mpfr.jl:831
  isfinite(::DataArrays.NAtype) at /Users/Alex/.julia/v0.6/DataArrays/src/predicates.jl:10
  ...
Stacktrace:
 [1] apply_statistic_typed(::Nullable{Int64}, ::Nullable{Int64}, ::Array{Nullable{Int64},1}, ::Array{Void,1}, ::Array{Void,1}) at /Users/Alex/.julia/v0.6/Gadfly/src/statistics.jl:909
 [2] apply_statistic(::Gadfly.Stat.TickStatistic, ::Dict{Symbol,Gadfly.ScaleElement}, ::Gadfly.Coord.Cartesian, ::Gadfly.Aesthetics) at /Users/Alex/.julia/v0.6/Gadfly/src/statistics.jl:772
 [3] apply_statistics(::Array{Gadfly.StatisticElement,1}, ::Dict{Symbol,Gadfly.ScaleElement}, ::Gadfly.Coord.Cartesian, ::Gadfly.Aesthetics) at /Users/Alex/.julia/v0.6/Gadfly/src/statistics.jl:40
 [4] render_prepare(::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:695
 [5] render(::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:748
 [6] display(::Base.REPL.REPLDisplay{Base.REPL.LineEditREPL}, ::MIME{Symbol("text/html")}, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:1062
 [7] display(::Base.REPL.REPLDisplay{Base.REPL.LineEditREPL}, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:1007
 [8] display(::Gadfly.Plot) at ./multimedia.jl:218
 [9] hookless(::Media.##7#8{Gadfly.Plot}) at /Users/Alex/.julia/v0.6/Media/src/compat.jl:14
 [10] render(::Media.NoDisplay, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Media/src/compat.jl:27
 [11] display(::Media.DisplayHook, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Media/src/compat.jl:9
 [12] display(::Gadfly.Plot) at ./multimedia.jl:218
 [13] eval(::Module, ::Any) at ./boot.jl:235
 [14] print_response(::Base.Terminals.TTYTerminal, ::Any, ::Void, ::Bool, ::Bool, ::Void) at ./REPL.jl:144
 [15] print_response(::Base.REPL.LineEditREPL, ::Any, ::Void, ::Bool, ::Bool) at ./REPL.jl:129
 [16] (::Base.REPL.#do_respond#16{Bool,Base.REPL.##26#36{Base.REPL.LineEditREPL,Base.REPL.REPLHistoryProvider},Base.REPL.LineEditREPL,Base.LineEdit.Prompt})(::Base.LineEdit.MIState, ::Base.AbstractIOBuffer{Array{UInt8,1}}, ::Bool) at ./REPL.jl:646
@alexomics
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Related to #909 ?

@Mattriks
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Mattriks commented Jan 2, 2018

Note that Gadfly has not supported the use of DataFrames with missing values (NA) for a while (#538, #567). Gadfly will produce an error on Julia v0.5 and v0.6 with the following example :

y = DataArray(randn(10))
y[5] = NA
D = DataFrame(x=[1:10;], y=y)
p = plot(D, x=:x, y=:y, Geom.line)

Does your DataFrame contain missing values, and can you provide a minimum example which produces the same error as you encountered.

@alexomics
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The DataFrame doesn't contain any missing values. I think the issue is stemming from using CSV. Manually creating small DataFrames doesn't produce the problem.

    julia> using CSV
    WARNING: Method definition ==(Base.Nullable{S}, Base.Nullable{T}) in module Base at nullable.jl:238 overwritten in module NullableArrays at /Users/Alex/.julia/v0.6/NullableArrays/src/operators.jl:99.
    
    julia> using DataFrames, Gadfly
    
    julia> poc = CSV.read("poc.csv");
    
    julia> poc
    6×2 DataFrames.DataFrame
    │ Row │ foo │ bar     │
    ├─────┼─────┼─────────┤
    │ 1   │ 521 │ 40.0    │
    │ 2   │ 521 │ 40.0003 │
    │ 3   │ 542 │ 40.0005 │
    │ 4   │ 540 │ 40.0007 │
    │ 5   │ 566 │ 40.001  │
    │ 6   │ 664 │ 40.0012 │
    
    julia> poc[:bar]
    6-element NullableArrays.NullableArray{Float64,1}:
     40.0
     40.0003
     40.0005
     40.0007
     40.001
     40.0012
    
    julia> poc[:foo]
    6-element NullableArrays.NullableArray{Int64,1}:
     521
     521
     542
     540
     566
     664
    
    julia> plot(poc, x=:bar, y=:foo, Geom.line)
    Error showing value of type Gadfly.Plot:
    ERROR: MethodError: no method matching isfinite(::Nullable{Float64})
    Closest candidates are:
      isfinite(::Float16) at float.jl:539
      isfinite(::BigFloat) at mpfr.jl:831
      isfinite(::DataArrays.NAtype) at /Users/Alex/.julia/v0.6/DataArrays/src/predicates.jl:10
      ...
    Stacktrace:
     [1] apply_statistic_typed(::Nullable{Float64}, ::Nullable{Float64}, ::Array{Nullable{Float64},1}, ::Array{Void,1}, ::Array{Void,1}) at /Users/Alex/.julia/v0.6/Gadfly/src/statistics.jl:909
     [2] apply_statistic(::Gadfly.Stat.TickStatistic, ::Dict{Symbol,Gadfly.ScaleElement}, ::Gadfly.Coord.Cartesian, ::Gadfly.Aesthetics) at /Users/Alex/.julia/v0.6/Gadfly/src/statistics.jl:772
     [3] apply_statistics(::Array{Gadfly.StatisticElement,1}, ::Dict{Symbol,Gadfly.ScaleElement}, ::Gadfly.Coord.Cartesian, ::Gadfly.Aesthetics) at /Users/Alex/.julia/v0.6/Gadfly/src/statistics.jl:40
     [4] render_prepare(::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:695
     [5] render(::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:748
     [6] display(::Base.REPL.REPLDisplay{Base.REPL.LineEditREPL}, ::MIME{Symbol("text/html")}, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:1062
     [7] display(::Base.REPL.REPLDisplay{Base.REPL.LineEditREPL}, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Gadfly/src/Gadfly.jl:1007
     [8] display(::Gadfly.Plot) at ./multimedia.jl:218
     [9] hookless(::Media.##7#8{Gadfly.Plot}) at /Users/Alex/.julia/v0.6/Media/src/compat.jl:14
     [10] render(::Media.NoDisplay, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Media/src/compat.jl:27
     [11] display(::Media.DisplayHook, ::Gadfly.Plot) at /Users/Alex/.julia/v0.6/Media/src/compat.jl:9
     [12] display(::Gadfly.Plot) at ./multimedia.jl:218
     [13] eval(::Module, ::Any) at ./boot.jl:235
     [14] print_response(::Base.Terminals.TTYTerminal, ::Any, ::Void, ::Bool, ::Bool, ::Void) at ./REPL.jl:144
     [15] print_response(::Base.REPL.LineEditREPL, ::Any, ::Void, ::Bool, ::Bool) at ./REPL.jl:129
     [16] (::Base.REPL.#do_respond#16{Bool,Base.REPL.##26#36{Base.REPL.LineEditREPL,Base.REPL.REPLHistoryProvider},Base.REPL.LineEditREPL,Base.LineEdit.Prompt})(::Base.LineEdit.MIState, ::Base.AbstractIOBuffer{Array{UInt8,1}}, ::Bool) at ./REPL.jl:646

@Mattriks
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Mattriks commented Jan 3, 2018

This works for me:

D = CSV.read("poc.csv", nullable=false)
p = plot(D, x=:bar, y=:foo, Geom.line)

See CSV documentation

@aterenin
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aterenin commented Jan 6, 2018

Confirmed same issue. There are no missing values in my data frame. Adding nullable=false fixes the error.

@tlnagy
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tlnagy commented Jan 6, 2018

Will the new missing code in Base help these problems?

@tlnagy tlnagy mentioned this issue Jan 11, 2018
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@Mattriks
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Since Julia 1.0 has a stable implementation of missing values, it would be worth supporting missing values in Gadfly now. This example already works:

D = DataFrame(x=1:10, y=randn(10))
allowmissing!(D)
D.y[5] = missing

p = plot(D, x=:x, y=:y, Geom.line)
draw(PNG(3.3inch,3.3inch), p)

iss1083a

But if you add Geom.point to the above code, it errors.

@Mattriks Mattriks mentioned this issue Mar 27, 2019
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@Mattriks
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Closing this is in favor of #1267

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4 participants
@tlnagy @aterenin @Mattriks @alexomics