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UndefRefError: access to undefined reference #3

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tk3369 opened this issue Apr 7, 2018 · 14 comments
Open

UndefRefError: access to undefined reference #3

tk3369 opened this issue Apr 7, 2018 · 14 comments

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@tk3369
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tk3369 commented Apr 7, 2018

Nice package, Mike! I found this obscure error message when saving this custom AbstractArray type from SASLib.jl.

julia> using SASLib

julia> p = SASLib.ObjectPool{String,UInt8}("", 3)
3-element SASLib.ObjectPool{String,UInt8}:
 ""
 ""
 ""

julia> BSON.@save "test.bson" p
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] lower(::Array{String,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/extensions.jl:60
 [2] _lower_recursive(::Array{String,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [3] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:25
 [4] _lower_recursive(::Array{Any,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [5] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:18
 [6] _lower_recursive(::Dict{String,UInt8}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [7] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:25
 [8] _lower_recursive(::Array{Any,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [9] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:18
 [10] _lower_recursive(::SASLib.ObjectPool{String,UInt8}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [11] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:18
 [12] _lower_recursive(::Dict{Symbol,SASLib.ObjectPool{String,UInt8}}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [13] lower_recursive(::Dict{Symbol,SASLib.ObjectPool{String,UInt8}}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:73
 [14] open(::BSON.##16#17{Dict{Symbol,SASLib.ObjectPool{String,UInt8}}}, ::String, ::String) at ./iostream.jl:152
 [15] bson(::String, ::Dict{Symbol,SASLib.ObjectPool{String,UInt8}}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:83
@MikeInnes
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Any chance you can narrow this down a bit? If you can figure out the minimal type definition that triggers this, it should be easy to fix.

@tk3369
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tk3369 commented Apr 20, 2018

Looks like it fails for all Dict with non-symbol keys:

julia> c4 = Dict("a" => :b)
Dict{String,Symbol} with 1 entry:
  "a" => :b

julia> BSON.@save "test.bson" c4
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] lower(::Array{String,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/extensions.jl:60
 [2] _lower_recursive(::Array{String,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [3] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:25
 [4] _lower_recursive(::Array{Any,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [5] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:18
 [6] _lower_recursive(::Dict{String,Symbol}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [7] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/tomkwong/.julia/v0.6/BSON/src/BSON.jl:18
 [8] _lower_recursive(::Dict{Symbol,Dict{String,Symbol}}, ::ObjectIdDict, ::Array{Any,1}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:62
 [9] lower_recursive(::Dict{Symbol,Dict{String,Symbol}}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:73
 [10] open(::BSON.##16#17{Dict{Symbol,Dict{String,Symbol}}}, ::String, ::String) at ./iostream.jl:152
 [11] bson(::String, ::Dict{Symbol,Dict{String,Symbol}}) at /Users/tomkwong/.julia/v0.6/BSON/src/write.jl:83

julia> c4 = Dict("a" => 1)
Dict{String,Int64} with 1 entry:
  "a" => 1

julia> BSON.@save "test.bson" c4
ERROR: UndefRefError: access to undefined reference

julia> c4 = Dict(1 => "a")
Dict{Int64,String} with 1 entry:
  1 => "a"

julia> BSON.@save "test.bson" c4
ERROR: UndefRefError: access to undefined reference

@DilumAluthge
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DilumAluthge commented May 16, 2018 •
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This is really interesting. It doesn't fail for all non-symbol keys; for example, it works for integer keys/integer values.

Key type Value type Does it work?
Symbol Symbol Yes
Symbol String Yes
Symbol Int64 Yes
String Symbol No
String String No
String Int64 No
Int64 Symbol No
Int64 String No
Int64 Int64 Yes 
julia> x1 = Dict(:a => :a); BSON.@save "test.bson" x1

julia> x2= Dict(:a => "a"); BSON.@save "test.bson" x2

julia> x3= Dict(:a => 1); BSON.@save "test.bson" x3

julia> x4 = Dict("a" => :a); BSON.@save "test.bson" x4
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] lower(::Array{String,1}) at /Users/dilum/.julia/v0.6/BSON/src/extensions.jl:60
 [2] _lower_recursive(::Array{String,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [3] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/BSON.jl:25
 [4] _lower_recursive(::Array{Any,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [5] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/dilum/.julia/v0.6/BSON/src/BSON.jl:18
 [6] _lower_recursive(::Dict{String,Symbol}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [7] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/dilum/.julia/v0.6/BSON/src/BSON.jl:18
 [8] _lower_recursive(::Dict{Symbol,Dict{String,Symbol}}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [9] lower_recursive(::Dict{Symbol,Dict{String,Symbol}}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:73
 [10] open(::BSON.##16#17{Dict{Symbol,Dict{String,Symbol}}}, ::String, ::String) at ./iostream.jl:152
 [11] bson(::String, ::Dict{Symbol,Dict{String,Symbol}}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:83

julia> x5 = Dict("a" => "a"); BSON.@save "test.bson" x5
ERROR: UndefRefError: access to undefined reference
Stacktrace:

julia> x6 = Dict("a" => 1); BSON.@save "test.bson" x6
ERROR: UndefRefError: access to undefined reference
Stacktrace:

julia> x7 = Dict(1 => :a); BSON.@save "test.bson" x7
ERROR: UndefRefError: access to undefined reference
Stacktrace:

julia> x8 = Dict(1 => "a"); BSON.@save "test.bson" x8
ERROR: UndefRefError: access to undefined reference
Stacktrace:

julia> x9 = Dict(1 => 1); BSON.@save "test.bson" x9

julia>

@DilumAluthge
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DilumAluthge commented May 26, 2018 •
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This works:

julia> BSON.bson("test.bson", Dict(:a => 1, :b => Dict(:c => 3, :d => Dict(:e => 5) )  ))

julia>

And this works:

julia> BSON.bson("test.bson", Dict(:a => 1, :b => Dict(:c => 3, :d => Dict(5 => 5) )  ))

julia>

And this also works:

julia> BSON.bson("test.bson", Dict(:a => 1, :b => Dict(:c => 3, :d => Dict(1.23 => 5) )  ))

julia>

But this does NOT work:

julia> BSON.bson("test.bson", Dict(:a => 1, :b => Dict(:c => 3, :d => Dict("e" => 5) )  ))
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] lower(::Array{String,1}) at /Users/dilum/.julia/v0.6/BSON/src/extensions.jl:60
 [2] _lower_recursive(::Array{String,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [3] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/BSON.jl:25
 [4] _lower_recursive(::Array{Any,1}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [5] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/dilum/.julia/v0.6/BSON/src/BSON.jl:18
 [6] _lower_recursive(::Dict{String,Int64}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [7] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/dilum/.julia/v0.6/BSON/src/BSON.jl:18
 [8] _lower_recursive(::Dict{Symbol,Any}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [9] applychildren!(::BSON.##7#11{ObjectIdDict,Array{Any,1}}, ::Dict{Symbol,Any}) at /Users/dilum/.julia/v0.6/BSON/src/BSON.jl:18
 [10] _lower_recursive(::Dict{Symbol,Any}, ::ObjectIdDict, ::Array{Any,1}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:62
 [11] lower_recursive(::Dict{Symbol,Any}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:73
 [12] open(::BSON.##16#17{Dict{Symbol,Any}}, ::String, ::String) at ./iostream.jl:152
 [13] bson(::String, ::Dict{Symbol,Any}) at /Users/dilum/.julia/v0.6/BSON/src/write.jl:83

julia>

@DilumAluthge
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So it looks like you can't have a dict with non-symbol keys anywhere inside the object you are trying to save - with the very weird exception of numerical keys and numerical values.

@DilumAluthge DilumAluthge mentioned this issue May 26, 2018
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@DilumAluthge
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DilumAluthge commented May 26, 2018 •
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I've found a hacky way to solve this issue - see PR #6.

@DilumAluthge DilumAluthge mentioned this issue May 31, 2018
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@DilumAluthge
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Disregard my previous comment - see better PR here: #7

@YingboMa
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The following code produces this error, too.

using StochasticDiffEq, BSON

function lorenz(du,u,p,t)
  du[1] = 10.0(u[2]-u[1])
  du[2] = u[1]*(28.0-u[3]) - u[2]
  du[3] = u[1]*u[2] - (8/3)*u[3]
end

function σ_lorenz(du,u,p,t)
  du[1] = 3.0
  du[2] = 3.0
  du[3] = 3.0
end

prob_sde_lorenz = SDEProblem(lorenz,σ_lorenz,[1.0,0.0,0.0],(0.0,10.0))
sol = solve(prob_sde_lorenz, SOSRA2())
bson("/tmp/test.bson",Dict(:sol=>sol))
julia> bson("/tmp/test.bson",Dict(:sol=>sol))
ERROR: UndefRefError: access to undefined reference
Stacktrace:
 [1] lower at /home/scheme/.julia/packages/BSON/kxdIr/src/extensions.jl:66 [inlined]
 [2] _lower_recursive(::Array{Tuple{Float64,Array{Float64,1},Array{Float64,1}},1}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [3] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::Array{Tuple{Float64,Array{Float64,1},Array{Float64,1}},1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [4] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:28
 [5] _lower_recursive(::Array{Any,1}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [6] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [7] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Dict{Symbol,Any}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:21
 [8] _lower_recursive(::DataStructures.DequeBlock{Tuple{Float64,Array{Float64,1},Array{Float64,1}}}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [9] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::DataStructures.DequeBlock{Tuple{Float64,Array{Float64,1},Array{Float64,1}}}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [10] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:28
 [11] _lower_recursive(::Array{Any,1}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [12] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [13] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Dict{Symbol,Any}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:21
 [14] _lower_recursive(::DataStructures.Deque{Tuple{Float64,Array{Float64,1},Array{Float64,1}}}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [15] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::DataStructures.Deque{Tuple{Float64,Array{Float64,1},Array{Float64,1}}}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [16] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:28
 [17] _lower_recursive(::Array{Any,1}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [18] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [19] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Dict{Symbol,Any}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:21
 [20] _lower_recursive(::DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [21] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [22] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:28
 [23] _lower_recursive(::Array{Any,1}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [24] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [25] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Dict{Symbol,Any}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:21
 [26] _lower_recursive(::DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [27] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [28] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:28
 [29] _lower_recursive(::Array{Any,1}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [30] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [31] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Dict{Symbol,Any}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:21
 [32] _lower_recursive(::RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Nothing,Nothing,SDEFunction{true,typeof(lorenz),typeof(σ_lorenz),UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(σ_lorenz),Nothing,Nothing},SOSRA2,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}}}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [33] (::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}})(::RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Nothing,Nothing,SDEFunction{true,typeof(lorenz),typeof(σ_lorenz),UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(σ_lorenz),Nothing,Nothing},SOSRA2,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}}}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [34] applychildren!(::getfield(BSON, Symbol("##7#11")){IdDict{Any,Any},Array{Any,1}}, ::Dict{Symbol,Any}) at /home/scheme/.julia/packages/BSON/kxdIr/src/BSON.jl:21
 [35] _lower_recursive(::Dict{Symbol,RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Nothing,Nothing,SDEFunction{true,typeof(lorenz),typeof(σ_lorenz),UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(σ_lorenz),Nothing,Nothing},SOSRA2,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}}}}, ::IdDict{Any,Any}, ::Array{Any,1}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:62
 [36] lower_recursive(::Dict{Symbol,RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Nothing,Nothing,SDEFunction{true,typeof(lorenz),typeof(σ_lorenz),UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(σ_lorenz),Nothing,Nothing},SOSRA2,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}}}}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:73
 [37] bson(::IOStream, ::Dict{Symbol,RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Nothing,Nothing,SDEFunction{true,typeof(lorenz),typeof(σ_lorenz),UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(σ_lorenz),Nothing,Nothing},SOSRA2,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}}}}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:81
 [38] #14 at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:83 [inlined]
 [39] #open#292(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::getfield(BSON, Symbol("##14#15")){Dict{Symbol,RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Nothing,Nothing,SDEFunction{true,typeof(lorenz),typeof(σ_lorenz),UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(σ_lorenz),Nothing,Nothing},SOSRA2,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}}}}}, ::String, ::Vararg{String,N} where N) at ./iostream.jl:369
 [40] open at ./iostream.jl:367 [inlined]
 [41] bson(::String, ::Dict{Symbol,RODESolution{Float64,2,Array{Array{Float64,1},1},Nothing,Nothing,Array{Float64,1},DiffEqNoiseProcess.NoiseProcess{Float64,2,Float64,Array{Float64,1},Array{Float64,1},Array{Array{Float64,1},1},typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_DIST),typeof(DiffEqNoiseProcess.INPLACE_WHITE_NOISE_BRIDGE),true,DataStructures.Stack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},ResettableStacks.ResettableStack{Tuple{Float64,Array{Float64,1},Array{Float64,1}}},DiffEqNoiseProcess.RSWM{:RSwM3,Float64},RandomNumbers.Xorshifts.Xoroshiro128Plus},SDEProblem{Array{Float64,1},Tuple{Float64,Float64},true,Nothing,Nothing,SDEFunction{true,typeof(lorenz),typeof(σ_lorenz),UniformScaling{Bool},Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing,Nothing},typeof(σ_lorenz),Nothing,Nothing},SOSRA2,StochasticDiffEq.LinearInterpolationData{Array{Array{Float64,1},1},Array{Float64,1}}}}) at /home/scheme/.julia/packages/BSON/kxdIr/src/write.jl:83
 [42] top-level scope at none:0

julia>

@devmotion
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The same error occurs when saving an optimizer in Flux: FluxML/Flux.jl#737

As far as I can see, the underlying problem is that it is not possible to save an IdDict.

@DilumAluthge
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Actually, the underlying problem here is that currently BSON.jl cannot handle arrays with undefined values. The issue for tracking this is: #43

Not being able to save certain Dicts is just a symptom of #43. The underlying implementation of Dict means that Dicts will often contain (under the hood) one or more Arrays with undefined values. In order to save/load the Dict, you need to be able to save/load the Arrays.

Once #43 is solved, there will be no problem saving/loading any kind of Dict.

@CarloLucibello
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examples in #3 (comment) all work now, this should be closed

@DilumAluthge
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DilumAluthge commented Apr 21, 2020 •
edited
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examples in #3 (comment) all work now, this should be closed

Before we close this issue, I think that we should take the examples from that issue and add them to the test suite of this package.

@kafisatz
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kafisatz commented Aug 3, 2020

I note that this error also happens in the absence of undef entries.
I ran into this with a dataframe column type

SentinelArrays.SentinelArray{String,1,UndefInitializer,Missing,Array{String,1}})

see JuliaData/SentinelArrays.jl#24 (comment)

@kafisatz kafisatz mentioned this issue Aug 3, 2020
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@umbriquse
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Also getting this error using the AbstractFFTs package.

using AbstractFFTs

a = FFTW.plan_fft(Array{Complex{Float64}}(undef,1))

var1 = Dict(:fft => a)

path = "_research/tmp/"
mkpath(path)

bson(path*"1.bson",var1)

typeof(a) = FFTW.cFFTWPlan{Complex{Float64},-1,false,1,UnitRange{Int64}}

I'm fairly new to Julia, so I'm not sure If there's more information I can provide to help pinpoint how/where this error is occurring.

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@devmotion @tk3369 @MikeInnes @DilumAluthge @CarloLucibello @kafisatz @YingboMa @umbriquse