Hi Avik,
Thank you for helping out.
I believe DataArrays is installed, at least interactively it seems to work. I'm
assuming in that case it is visible in SerialMC as well?
Is it normal there are 2 versions reported in Pkg.available("DataArrays")?
Rob J. Goedman
[email protected]
On Jan 17, 2014, at 10:40 AM, Avik Sengupta <[email protected]> wrote:
> This has come up a few times recently, but I am not sure why the DataArrays
> package doesn't get installed (it should due to the dependency resolution).
> The workaround is to force install of the that package
>
> Pkg.add("DataArrays")
robs-15inch-2:~ rob$ exec
'/Applications/Julia-0.2.0.app/Contents/Resources/julia/bin/julia'
_
_ _ _(_)_ | A fresh approach to technical computing
(_) | (_) (_) | Documentation: http://docs.julialang.org
_ _ _| |_ __ _ | Type "help()" to list help topics
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 0.2.0 (2013-11-16 23:44 UTC)
_/ |\__'_|_|_|\__'_| | Official http://julialang.org release
|__/ | x86_64-apple-darwin12.5.0
julia> Pkg.update()
INFO: Updating METADATA...
INFO: Updating DataArrays...
INFO: Updating Stats...
INFO: Computing changes...
INFO: No packages to install, update or remove.
julia> Pkg.add("DataArrays")
INFO: Nothing to be done.
julia> Pkg.add("DataFrames")
INFO: Nothing to be done.
julia> Pkg.add("Stats")
INFO: Nothing to be done.
julia> Pkg.add("MCMC")
INFO: Nothing to be done.
julia> using Rmath,DataArrays,DataFrames,Stats,Distributions,MCMC
Warning: could not import Base.foldl into NumericExtensions
Warning: could not import Base.foldr into NumericExtensions
Warning: could not import Base.sum! into NumericExtensions
Warning: could not import Base.maximum! into NumericExtensions
Warning: could not import Base.minimum! into NumericExtensions
Warning: could not import Base.PAIRWISE_SUM_BLOCKSIZE into NumericExtensions
Loading MCMCLikModel model
Loading RWM(scale, tuner) sampler
Loading RAM(scale, rate) sampler
Loading MALA(driftStep, tuner) sampler
Loading HMC(nLeaps, leapStep, tuner) sampler
Loading HMCDA(rate, len, shrinkage, t0, step) sampler
Loading NUTS(maxdoublings, tuner) sampler
Loading SMMALA(driftStep, tuner) sampler
Loading PMALA(driftStep, tuner) sampler
Loading RMHMC(nLeaps, leapStep, nNewton, tuner) sampler
Loading ERMLMC(nLeaps, leapStep, tuner) sampler
Loading SerialMC(steps, burnin, thinning) runner
Loading SerialTempMC(steps, burnin, swapPeriod) runner
Loading SeqMC(steps, burnin, trigger) runner
julia> Pkg.available("DataArrays")
2-element Array{VersionNumber,1}:
v"0.0.0"
v"0.0.1"
julia> n = 8
8
julia> float64(DataArray(zeros(Float64 ,n)))
8-element DataArray{Float64,1}:
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
julia> mymodel1 = model(v->-dot(v,v), init=ones(3))
WARNING: assert(x,y) is deprecated, use @assert x y instead.
in depwarn at deprecated.jl:29
in assert at deprecated.jl:19
in MCMCLikelihoodModel at /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:43
in MCMCLikelihoodModel at /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:129
in model at /Users/rob/.julia/MCMC/src/modellers/mcmcmodels.jl:39
WARNING: assert(x,y) is deprecated, use @assert x y instead.
in depwarn at deprecated.jl:29
in assert at deprecated.jl:19
in MCMCLikelihoodModel at /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:44
in MCMCLikelihoodModel at /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:129
in model at /Users/rob/.julia/MCMC/src/modellers/mcmcmodels.jl:39
MCMCLikelihoodModel((anonymous
function),nothing,nothing,nothing,nothing,nothing,nothing,[:pars=>PDims(1,(3,))],3,[1.0,1.0,1.0],[1.0,1.0,1.0])
julia> mychain=run(mymodel1,RWM(0.1), SerialMC(steps=1000,burnin=100))
WARNING: assert(x,y) is deprecated, use @assert x y instead.
in depwarn at deprecated.jl:29
in assert at deprecated.jl:19
in RWM at /Users/rob/.julia/MCMC/src/samplers/RWM.jl:29
in RWM at /Users/rob/.julia/MCMC/src/samplers/RWM.jl:34
ERROR: DataArray not defined
in run_serialmc at /Users/rob/.julia/MCMC/src/runners/SerialMC.jl:61
in run at /Users/rob/.julia/MCMC/src/runners/runners.jl:9
in run at /Users/rob/.julia/MCMC/src/runners/runners.jl:45
julia>
>
> On Friday, 17 January 2014 17:18:17 UTC, Rob J Goedman wrote:
> Hi,
>
> I'm wondering if I have mixed versions installed, e.g. the initial MCMC
> example below shows a couple of warnings and an error on DataArray.
>
> Any hints?
>
> Thanks,
> Rob
>
> Mac OSX 10.9.2, Xcode 5.1Beta3 + command line tools
>
> robs-15inch-2:~ rob$ exec
> '/Applications/Julia-0.2.0.app/Contents/Resources/julia/bin/julia'
> _
> _ _ _(_)_ | A fresh approach to technical computing
> (_) | (_) (_) | Documentation: http://docs.julialang.org
> _ _ _| |_ __ _ | Type "help()" to list help topics
> | | | | | | |/ _` | |
> | | |_| | | | (_| | | Version 0.2.0 (2013-11-16 23:44 UTC)
> _/ |\__'_|_|_|\__'_| | Official http://julialang.org release
> |__/ | x86_64-apple-darwin12.5.0
>
> julia> using MCMC
> Loading MCMCLikModel model
> Loading RWM(scale, tuner) sampler
> Loading RAM(scale, rate) sampler
> Loading MALA(driftStep, tuner) sampler
> Loading HMC(nLeaps, leapStep, tuner) sampler
> Loading HMCDA(rate, len, shrinkage, t0, step) sampler
> Loading NUTS(maxdoublings, tuner) sampler
> Loading SMMALA(driftStep, tuner) sampler
> Loading PMALA(driftStep, tuner) sampler
> Loading RMHMC(nLeaps, leapStep, nNewton, tuner) sampler
> Loading ERMLMC(nLeaps, leapStep, tuner) sampler
> Loading SerialMC(steps, burnin, thinning) runner
> Loading SerialTempMC(steps, burnin, swapPeriod) runner
> Loading SeqMC(steps, burnin, trigger) runner
>
> julia> using DataArrays
>
> julia> mymodel2 = model(v->-dot(v,v),grad=v->-v,init=ones(3))
> WARNING: assert(x,y) is deprecated, use @assert x y instead.
> in depwarn at deprecated.jl:29
> in assert at deprecated.jl:19
> in MCMCLikelihoodModel at /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:43
> in MCMCLikelihoodModel at
> /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:129
> in model at /Users/rob/.julia/MCMC/src/modellers/mcmcmodels.jl:39
> WARNING: assert(x,y) is deprecated, use @assert x y instead.
> in depwarn at deprecated.jl:29
> in assert at deprecated.jl:19
> in MCMCLikelihoodModel at /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:44
> in MCMCLikelihoodModel at
> /Users/rob/.julia/MCMC/src/modellers/likmodel.jl:129
> in model at /Users/rob/.julia/MCMC/src/modellers/mcmcmodels.jl:39
> MCMCLikelihoodModel((anonymous function),(anonymous
> function),nothing,nothing,(anonymous
> function),nothing,nothing,[:pars=>PDims(1,(3,))],3,[1.0,1.0,1.0],[1.0,1.0,1.0])
>
> julia> mychain=run(mymodel2,RWM(0.1), SerialMC(steps=1000,burnin=100))
> WARNING: assert(x,y) is deprecated, use @assert x y instead.
> in depwarn at deprecated.jl:29
> in assert at deprecated.jl:19
> in RWM at /Users/rob/.julia/MCMC/src/samplers/RWM.jl:29
> in RWM at /Users/rob/.julia/MCMC/src/samplers/RWM.jl:34
> ERROR: DataArray not defined
> in run_serialmc at /Users/rob/.julia/MCMC/src/runners/SerialMC.jl:61
> in run at /Users/rob/.julia/MCMC/src/runners/runners.jl:9
> in run at /Users/rob/.julia/MCMC/src/runners/runners.jl:45
>
> julia>
>
