Chris, Do you mind continuing this discussion in issue # 1 of Stan.jl as it is exactly the issue Doug raised there.
I’ve not helped by recently upgrading Stan.jl to work on Julia 0.5 and now a new install on Julia 0.4 gets the ‘old’ Stan 0.3.2 and Pkg.checkout(“Stan”) won’t work anymore on Julia 0.5 nor contain fixes as provided by Doug and Tomas for non-OSX usage. The warning are ok for now (mostly switching packages to Julia 0.5- related). Can you edit src/Stan.jl in .julia/v0.4/Stan? If so, you could insert a line like: global const CMDSTAN_HOME = ENV["CMDSTAN_HOME"] Regards, Rob > On Sep 1, 2016, at 07:15, Christopher Fisher <[email protected]> wrote: > > Once again, thanks for your help. After mastering the installation on Mac, > Linux seems to be a bit more tricky. Here is what I get after calling Stan > > > WARNING: New definition > +(AbstractArray, DataArrays.DataArray) at > /home/dfish/.julia/v0.4/DataArrays/src/operators.jl:276 > is ambiguous with: > +(WoodburyMatrices.SymWoodbury, AbstractArray{T<:Any, 2}) at > /home/dfish/.julia/v0.4/WoodburyMatrices/src/SymWoodburyMatrices.jl:107. > To fix, define > +(WoodburyMatrices.SymWoodbury, DataArrays.DataArray{T<:Any, 2}) > before the new definition. > WARNING: New definition > +(AbstractArray, DataArrays.AbstractDataArray) at > /home/dfish/.julia/v0.4/DataArrays/src/operators.jl:300 > is ambiguous with: > +(WoodburyMatrices.SymWoodbury, AbstractArray{T<:Any, 2}) at > /home/dfish/.julia/v0.4/WoodburyMatrices/src/SymWoodburyMatrices.jl:107. > To fix, define > +(WoodburyMatrices.SymWoodbury, DataArrays.AbstractDataArray{T<:Any, 2}) > before the new definition. > WARNING: Base.String is deprecated, use AbstractString instead. > likely near /home/dfish/.julia/v0.4/Graphs/src/common.jl:3 > WARNING: Base.String is deprecated, use AbstractString instead. > likely near /home/dfish/.julia/v0.4/Graphs/src/dot.jl:80 > WARNING: New definition > promote_rule(Type{Mamba.ScalarLogical}, Type{##267#T<:Real}) at > /home/dfish/.julia/v0.4/Mamba/src/variate.jl:20 > is ambiguous with: > promote_rule(Type{#A<:Real}, Type{ForwardDiff.Dual{#N<:Any, #B<:Real}}) > at /home/dfish/.julia/v0.4/ForwardDiff/src/dual.jl:154. > To fix, define > promote_rule(Type{Mamba.ScalarLogical}, Type{ForwardDiff.Dual{#N<:Any, > #B<:Real}}) > before the new definition. > WARNING: New definition > promote_rule(Type{Mamba.ScalarStochastic}, Type{##270#T<:Real}) at > /home/dfish/.julia/v0.4/Mamba/src/variate.jl:20 > is ambiguous with: > promote_rule(Type{#A<:Real}, Type{ForwardDiff.Dual{#N<:Any, #B<:Real}}) > at /home/dfish/.julia/v0.4/ForwardDiff/src/dual.jl:154. > To fix, define > promote_rule(Type{Mamba.ScalarStochastic}, Type{ForwardDiff.Dual{#N<:Any, > #B<:Real}}) > before the new definition. > > > Environment variable CMDSTAN_HOME not found. > Environment variable JULIA_SVG_BROWSER not found. > > I'm not sure what the first warning is exactly. I get that for Gadfly but it > seems not to affect its functionality. > > When I submit CMDSTAN_HOME I get: > > " " > > Based on your folder structure, I pointed my variable to > > CMDSTAN_HOME="/home/dfish/cmdstan-2.11.0" > > in the juliarc.jl file. > > A picture of my folder structure is included as an attachment. > > Thanks, > > Chris > > > > On Thursday, September 1, 2016 at 9:36:50 AM UTC-4, Rob J Goedman wrote: > Hi Chris, > > Can you see what Ubuntu comes up with after: > > > julia> using Stan > INFO: Recompiling stale cache file > /Users/rob/.julia/lib/v0.5/Distributions.ji for module Distributions. > INFO: Recompiling stale cache file /Users/rob/.julia/lib/v0.5/DataArrays.ji > for module DataArrays. > INFO: Recompiling stale cache file /Users/rob/.julia/lib/v0.5/Gadfly.ji for > module Gadfly. > INFO: Recompiling stale cache file /Users/rob/.julia/lib/v0.5/DataFrames.ji > for module DataFrames. > INFO: Recompiling stale cache file > /Users/rob/.julia/lib/v0.5/KernelDensity.ji for module KernelDensity. > > julia> CMDSTAN_HOME > "/Users/rob/Projects/Stan/cmdstan" > > This should point to the top level: > > > > Regards, > Rob > >> On Sep 1, 2016, at 03:24, Christopher Fisher <fish...@ <>miamioh.edu >> <http://miamioh.edu/>> wrote: >> >> Correction. The paths should have " " around them. >> >> On Thursday, September 1, 2016 at 6:19:00 AM UTC-4, Christopher Fisher wrote: >> Also, I've tried adding a path in the .juliarc file. Its not clear to me >> what subfolder in cmd stan it should point to, so I tried the following to >> no avail: >> >> CMDSTAN_HOME=/home/dfish/cmdstan-2.11.0/stan_2.11.0 >> >> CMDSTAN_HOME=/home/dfish/cmdstan-2.11.0/src/cmdstan >> >> CMDSTAN_HOME=/home/dfish/cmdstan-2.11.0/stan_2.11.0 >> >> >> On Thursday, September 1, 2016 at 5:55:50 AM UTC-4, Christopher Fisher wrote: >> I am encountering a problem while trying to interface Stan through Julia. >> Right now I am using Julia .4.6, Stan .3.2, Mamba .9.2 and Ubuntu 16.04. I >> have successfully installed cmd Stan and ran the Bernoulli test model. >> However, when I run Pkg.test("Stan") I get the following error: >> >> Environment variable CMDSTAN_HOME not found. >> Environment variable JULIA_SVG_BROWSER not found. >> >> Based on the Mac instructions, I tried placing the following in the .bashrc >> file >> >> export STAN_HOME=/home/dfish/cmdstan-2.11.0/stan_2.11.0/stan >> export CMDSTAN_HOME=/home/dfish/cmdstan-2.11.0/stan_2.11.0 >> export JAGS_HOME=/usr/local/bin/jags >> >> Perhaps not surprisingly, that did not work. Any help would be appreciated. >> >> -Chris > > <Stan Folders>
