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
> <javascript:>> 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
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