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JuliaPlots / StatsPlots.jl

Statistical plotting recipes for Plots.jl
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Error plotting MCMCChains #495

Closed rkube closed 2 years ago

rkube commented 2 years ago

Hi, I'm trying to plot an MCMCChain, calling plot(chain), in vscode and receive the error message below. Plotting in general works fine. The same GKS error also occurs in the repl outside vscode but there is no stacktrace.

using Turing, Distributions
using CSV
using DataFrames
using MCMCChains, Plots, StatsPlots
using Random
Random.seed!(0)

df = CSV.read("data/howell.csv", DataFrame)
gdf = filter(:age => x -> x > 18, df)

@model function linear_model(x, y)
    # Set variance prior
    σ2 ~ Uniform(0.0, 10.0);
    α ~ Normal(60, 10);
    nfeatures=size(x)
    β ~ MvLogNormal(zeros(nfeatures), ones(nfeatures));
    μ = α .+ β .* (x .- mean(x));
    y ~ MvNormal(μ, sqrt(σ2));
end

model = linear_model(gdf[!, :height], gdf[!, :weight])
chain = sample(model, NUTS(0.65), 1_000);
plot(chain)

GKS: Rectangle definition is invalid in routine SET_VIEWPORT GKS: Rectangle definition is invalid in routine SET_VIEWPORT [...] Repeats a lot ... GKS: Rectangle definition is invalid in routine SET_VIEWPORT ERROR: SystemError: opening file "/var/folders/2p/kw9s71xx0fl6c0_t44p9lb580000gn/T/jl_JP1zoR.png": No such file or directory Stacktrace: [1] systemerror(p::String, errno::Int32; extrainfo::Nothing) @ Base ./error.jl:174 [2] #systemerror#68 @ ./error.jl:173 [inlined] [3] systemerror @ ./error.jl:173 [inlined] [4] open(fname::String; lock::Bool, read::Nothing, write::Nothing, create::Nothing, truncate::Nothing, append::Nothing) @ Base ./iostream.jl:293 [5] open @ ./iostream.jl:282 [inlined] [6] open(f::Base.var"#364#365"{String}, args::String; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Base ./io.jl:328 [7] open @ ./io.jl:328 [inlined] [8] read @ ./io.jl:436 [inlined] [9] _show(io::Base64.Base64EncodePipe, #unused#::MIME{Symbol("image/png")}, plt::Plots.Plot{Plots.GRBackend}) @ Plots ~/.julia/packages/Plots/dNEbX/src/backends/gr.jl:2171 [10] show(io::Base64.Base64EncodePipe, m::MIME{Symbol("image/png")}, plt::Plots.Plot{Plots.GRBackend}) @ Plots ~/.julia/packages/Plots/dNEbX/src/output.jl:212 [11] base64encode(::Function, ::MIME{Symbol("image/png")}, ::Vararg{Any}; context::Nothing) @ Base64 /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Base64/src/encode.jl:209 [12] _binstringmime @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Base64/src/Base64.jl:46 [inlined] [13] stringmime(m::MIME{Symbol("image/png")}, x::Plots.Plot{Plots.GRBackend}; context::Nothing) @ Base64 /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Base64/src/Base64.jl:43 [14] stringmime @ /Applications/Julia-1.7.app/Contents/Resources/julia/share/julia/stdlib/v1.7/Base64/src/Base64.jl:43 [inlined] [15] display(d::VSCodeServer.InlineDisplay, m::MIME{Symbol("image/png")}, x::Plots.Plot{Plots.GRBackend}) @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/display.jl:57 [16] display(d::VSCodeServer.InlineDisplay, mime::String, x::Any) @ Base.Multimedia ./multimedia.jl:216 [17] display(d::VSCodeServer.InlineDisplay, x::Plots.Plot{Plots.GRBackend}) @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/display.jl:165 [18] display(x::Any) @ Base.Multimedia ./multimedia.jl:328 [19] #invokelatest#2 @ ./essentials.jl:716 [inlined] [20] invokelatest @ ./essentials.jl:714 [inlined] [21] (::VSCodeServer.var"#65#69"{Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})() @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/eval.jl:176 [22] withpath(f::VSCodeServer.var"#65#69"{Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams}, path::String) @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/repl.jl:184 [23] (::VSCodeServer.var"#64#68"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})() @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/eval.jl:153 [24] hideprompt(f::VSCodeServer.var"#64#68"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams}) @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/repl.jl:36 [25] (::VSCodeServer.var"#63#67"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})() @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/eval.jl:124 [26] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:511 [27] with_logger @ ./logging.jl:623 [inlined] [28] (::VSCodeServer.var"#62#66"{VSCodeServer.ReplRunCodeRequestParams})() @ VSCodeServer ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/eval.jl:201 [29] #invokelatest#2 @ ./essentials.jl:716 [inlined] [30] invokelatest(::Any) @ Base ./essentials.jl:714 [31] macro expansion @ ~/.vscode/extensions/julialang.language-julia-1.6.17/scripts/packages/VSCodeServer/src/eval.jl:34 [inlined] [32] (::VSCodeServer.var"#60#61")() @ VSCodeServer ./task.jl:423

julia>

rkube commented 2 years ago

Oh, I had an error in the model. Using β ~ LogNormal(0.0, 1.0); the error disappears.