I see, but I thought I'd like to try and remove the instability as I wonder 
if it's one of the things preventing vectorisation of the @inbounds loop in 
the `distance` function.

On Friday, September 16, 2016 at 7:54:33 AM UTC+1, Kristoffer Carlsson 
wrote:
>
> It looks fine because for both the SSAValues with "problems" you later 
> have:
>
>  p::Array{Float64,1} = SSAValue(15)
>
>  l::Array{Int64,1} = SSAValue(17)
>
> so they actually get correctly inferred.
>
> As long as your variables list and return value is ok then things are most 
> likely ok.
>
> On Friday, September 16, 2016 at 4:37:09 AM UTC+2, Yichao Yu wrote:
>>
>> On Thu, Sep 15, 2016 at 10:08 AM, Ben Ward <axolotl...@gmail.com> wrote: 
>> > 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}} 
>>
>> I guess we should probably print ssavalue types to make this easier to 
>> analyse 
>>
>> There's likely no type instability and the warning here is just spurious 
>>
>> > 
>> >       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. 
>>
>

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