[julia-users] Tracking down type instability

[Ben Ward]

Hi I have two functions and a function which calls them:

@inline function expected_distance(::Type{JukesCantor69}, p::Float64)
    return -0.75 * log(1 - 4 * p / 3)
end

@inline function variance(::Type{JukesCantor69}, p::Float64, l::Int64)
    return p * (1 - p) / (((1 - 4 * p / 3) ^ 2) * l)
end

function distance{A<:NucleotideAlphabet}(::Type{JukesCantor69}, 
seqs::Vector{BioSequence{A}})
    p, l = distance(Proportion{AnyMutation}, seqs)
    D = Vector{Float64}(length(p))
    V = Vector{Float64}(length(p))
    @inbounds for i in 1:length(p)
        D[i] = expected_distance(JukesCantor69, p[i])
        V[i] = variance(JukesCantor69, p[i], l[i])
    end
    return D, V
end

But I'm seeing type uncertainty:

*@code_warntype distance(JukesCantor69, dnas)*

Variables:

  #self#::Bio.Var.#distance

  #unused#::Type{Bio.Var.JukesCantor69}

  seqs::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1}

  p::Array{Float64,1}

  l::Array{Int64,1}

  #temp#@_6::Int64

  D::Array{Float64,1}

  V::Array{Float64,1}

  #temp#@_9::Int64

  i::Int64


Body:

  begin 

      SSAValue(0) = $(Expr(:invoke, LambdaInfo for 
distance(::Type{Bio.Var.Proportion{Bio.Var.AnyMutation}}, 
::Array{Bio.Seq.BioSequence{Bio.Seq.DNAAlphabet{4}},1}), 
:(Bio.Var.distance), Bio.Var.Proportion{Bio.Var.AnyMutation}, :(seqs)))

      #temp#@_6::Int64 = $(QuoteNode(1))

      SSAValue(15) = (Base.getfield)(SSAValue(0),1)
*::Union{Array{Float64,1},Array{Int64,1}}*

      SSAValue(16) = (Base.box)(Int64,(Base.add_int)(1,1))

      p::Array{Float64,1} = SSAValue(15)

      #temp#@_6::Int64 = SSAValue(16)

      SSAValue(17) = (Base.getfield)(SSAValue(0),2)
*::Union{Array{Float64,1},Array{Int64,1}}*

      SSAValue(18) = (Base.box)(Int64,(Base.add_int)(2,1))

      l::Array{Int64,1} = SSAValue(17)

      #temp#@_6::Int64 = SSAValue(18) # line 314:

      SSAValue(7) = (Base.arraylen)(p::Array{Float64,1})::Int64

      D::Array{Float64,1} = 
(Core.ccall)(:jl_alloc_array_1d,(Core.apply_type)(Core.Array,Float64,1)::Type{Array{Float64,1}},(Core.svec)(Core.Any,Core.Int)::SimpleVector,Array{Float64,1},0,SSAValue(7),0)::Array{Float64,1}
 
# line 315:

      SSAValue(9) = (Base.arraylen)(p::Array{Float64,1})::Int64

      V::Array{Float64,1} = 
(Core.ccall)(:jl_alloc_array_1d,(Core.apply_type)(Core.Array,Float64,1)::Type{Array{Float64,1}},(Core.svec)(Core.Any,Core.Int)::SimpleVector,Array{Float64,1},0,SSAValue(9),0)::Array{Float64,1}
 
# line 316:

      $(Expr(:inbounds, true))

      SSAValue(11) = (Base.arraylen)(p::Array{Float64,1})::Int64

      SSAValue(19) = 
(Base.select_value)((Base.sle_int)(1,SSAValue(11))::Bool,SSAValue(11),(Base.box)(Int64,(Base.sub_int)(1,1)))::Int64

      #temp#@_9::Int64 = 1

      22: 

      unless (Base.box)(Base.Bool,(Base.not_int)((#temp#@_9::Int64 === 
(Base.box)(Int64,(Base.add_int)(SSAValue(19),1)))::Bool)) goto 43

      SSAValue(20) = #temp#@_9::Int64

      SSAValue(21) = (Base.box)(Int64,(Base.add_int)(#temp#@_9::Int64,1))

      i::Int64 = SSAValue(20)

      #temp#@_9::Int64 = SSAValue(21) # line 317:

      SSAValue(12) = (Base.arrayref)(p::Array{Float64,1},i::Int64)::Float64

      $(Expr(:inbounds, false))

      # meta: location /Users/bward/.julia/v0.5/Bio/src/var/distances.jl 
expected_distance 69

      SSAValue(13) = $(Expr(:invoke, LambdaInfo for log(::Float64), 
:(Bio.Var.log), 
:((Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),(Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)((Base.box)(Float64,(Base.sitofp)(Float64,4)),SSAValue(12))),(Base.box)(Float64,(Base.sitofp)(Float64,3)))))))))

      # meta: pop location

      $(Expr(:inbounds, :pop))

      SSAValue(5) = 
(Base.box)(Base.Float64,(Base.mul_float)(-0.75,SSAValue(13)))

      
(Base.arrayset)(D::Array{Float64,1},SSAValue(5),i::Int64)::Array{Float64,1} 
# line 318:

      SSAValue(14) = (Base.arrayref)(p::Array{Float64,1},i::Int64)::Float64

      SSAValue(6) = 
(Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)(SSAValue(14),(Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),SSAValue(14))))),(Base.box)(Base.Float64,(Base.mul_float)((Base.Math.box)(Base.Math.Float64,(Base.Math.powi_llvm)((Base.box)(Base.Float64,(Base.sub_float)((Base.box)(Float64,(Base.sitofp)(Float64,1)),(Base.box)(Base.Float64,(Base.div_float)((Base.box)(Base.Float64,(Base.mul_float)((Base.box)(Float64,(Base.sitofp)(Float64,4)),SSAValue(14))),(Base.box)(Float64,(Base.sitofp)(Float64,3)))))),(Base.box)(Int32,(Base.checked_trunc_sint)(Int32,2))))::Float64,(Base.box)(Float64,(Base.sitofp)(Float64,(Base.arrayref)(l::Array{Int64,1},i::Int64)::Int64))))))

      
(Base.arrayset)(V::Array{Float64,1},SSAValue(6),i::Int64)::Array{Float64,1}

      41: 

      goto 22

      43: 

      $(Expr(:inbounds, :pop)) # line 320:

      return 
(Core.tuple)(D::Array{Float64,1},V::Array{Float64,1})::Tuple{Array{Float64,1},Array{Float64,1}}

  end::Tuple{Array{Float64,1},Array{Float64,1}}

But I'm not sure which those lines correspond to in my code, as they're 
temporary values. I think at some point some code either results in an 
integer or a float. I wondered if it was inside the smaller function called 
by the larger one.

Thanks,
Ben.