[R] How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009
Paul Heinrich Dietrich
paul.heinrich.dietrich at gmail.com
Fri Feb 20 00:44:49 CET 2009
Hi Kees,
No harm no foul. I'm glad you posted that anyway, because now anyone who's
trying to do the same thing and read this will know to seek your 1.1.9
version and stay away from 1.1.15.
Paul
chaogai-2 wrote:
>
> I do not know about the ubuntu instructions, they would not help me on
> Suse. The wine version is 1.1.9.
> I thought that was the latest,but when I checked latest is 1.1.15, which
> does indeed throw the blackbox error.
> So, now it does not work for me either
> Sorry I gave bad advise
>
> kees
>
> On Thu, 19 Feb 2009 01:38:15 +0100, Paul Heinrich Dietrich
> <paul.heinrich.dietrich at gmail.com> wrote:
>
>>
>> I went to this webpage (http://ubuntuforums.org/showthread.php?t=624644)
>> and
>> followed the instructions to the letter on getting the latest Wine. I
>> installed WinBUGS again, but this time I cannot open it in Wine. It says
>> Black Box, Trap #101, and some text I can't copy/paste here. Is this the
>> latest Wine that you have, or something different? Thanks.
>>
>>
>> chaogai-2 wrote:
>>>
>>> Hi,
>>>
>>> For me running winbugs through wine just works. Even when I do not
>>> specify
>>> any directories.
>>> The example they give in the bugs helpfile was my starting point.
>>> Setup is suse 11.1, latest Wine, R, R2WinBUGS & winbugs.
>>> I assume you first tried without specifying directories?
>>> The directories you use do not work for me, with WINEPATH the culprit.
>>> If you do not have the latest wine I advise to upgrade & not specify
>>> directories.
>>>
>>> Good luck,
>>> Kees
>>>
>>> On Wed, 18 Feb 2009 01:27:18 +0100, Paul Heinrich Dietrich
>>> <paul.heinrich.dietrich at gmail.com> wrote:
>>>
>>>>
>>>> Hi Uwe,
>>>> Thank you for your guidance. I have installed R2WinBUGS and WinBUGS14
>>>> under
>>>> wine. Using ?bugs for help, it tells me:
>>>>
>>>> useWINE: logical; attempt to use the Wine emulator to run 'WinBUGS',
>>>> defaults to 'FALSE' on Windows, and 'TRUE' otherwise. Not available in
>>>> S-PLUS.
>>>>
>>>> WINE: character, path to 'wine' binary file, it is tried hard (by a
>>>> guess
>>>> and the utilities 'which' and 'locate') to get the information
>>>> automatically if not given.
>>>>
>>>> newWINE: Use new versions of Wine that have 'winepath' utility
>>>>
>>>> WINEPATH: character, path to 'winepath' binary file, it is tried hard
>>>> (by a
>>>> guess and the utilities 'which' and 'locate') to get the information
>>>> automatically if not given.
>>>>
>>>> ..and the following code is a simple Bayesian version of a t-test...
>>>>
>>>> ############################ Directory Paths
>>>> ############################
>>>> MyModelPath <- "/home/me/Compound/R/WinBUGS/"
>>>> MyBUGSPath <- "/home/me/.wine/drive_c/Program Files/WinBUGS14/"
>>>> MyModelFile <- paste(MyModelPath, "model.bug", sep="")
>>>> WINEPATH <- "/usr/bin/wine"
>>>>
>>>> ############################ Create Data Set
>>>> ############################
>>>> # Here is some fake data
>>>> n_draws <- 50
>>>> x <- round(runif(n_draws, 1, 2))
>>>> y <- ifelse(x == 1, rnorm(n_draws, 1, 1), rnorm(n_draws, 1.2, 0.8))
>>>> MyData <- as.data.frame(cbind(y, x))
>>>> y.n <- NROW(MyData$y)
>>>> x.j <- length(unique(x))
>>>> summary(MyData)
>>>>
>>>> ###################### Format Data for WinBUGS
>>>> ##########################
>>>> MyBUGSData <- list(y=MyData$y, x=MyData$x, n=y.n, x.j=x.j)
>>>> MyBUGSData
>>>>
>>>> ########################## WinBUGS Model File
>>>> ###########################
>>>> library(R2WinBUGS)
>>>> cat("model
>>>> {
>>>> for (i in 1:n)
>>>> {
>>>> y[i] ~ dnorm(mu[i], tau)
>>>> mu[i] <- alpha + beta[x[i]]
>>>> }
>>>> ### STZ (Sum-To-Zero) Constraints
>>>> beta[1] <- -sum(beta[2:x.j])
>>>> ### Priors
>>>> alpha ~ dnorm(0.0, 1.0E-4)
>>>> for (i in 2:x.j)
>>>> {
>>>> beta[i] ~ dnorm(0.0, 1.0E-4)
>>>> }
>>>> tau ~ dgamma(0.01, 0.01)
>>>> precision <- sqrt(1/tau)
>>>> }",
>>>> file=MyModelFile)
>>>> file.show(MyModelFile)
>>>>
>>>> ############################# WinBUGS Model
>>>> #############################
>>>> MyModel <- bugs(MyBUGSData, inits=NULL,
>>>> model.file=MyModelFile,
>>>> parameters.to.save=c("alpha", "beta", "precision"),
>>>> n.chains=3, n.iter=2000, n.burnin=1000, n.thin=1, codaPkg=TRUE,
>>>> bugs.directory = MyBUGSPath, working.directory=MyModelPath,
>>>> useWINE=TRUE, WINEPATH=WINEPATH, debug=TRUE)
>>>>
>>>> The output says:
>>>>
>>>> ERROR:
>>>> cannot open the connection
>>>>
>>>> I'm wondering if I've misinterpreted how to set my paths with wine,
>>>> because
>>>> I can go to the following path, double-click on WinBUGS14.exe, and open
>>>> it
>>>> just fine: /home/me/.wine/drive_c/Program Files/WinBUGS14/
>>>>
>>>> I can also go to Applications > Wine > Browse C:\ Drive and navigate to
>>>> WinBUGS.
>>>>
>>>> Please help if I've done something wrong. Thanks.
>>>
>>>
>>>
>>> --
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>>
>>
>
>
>
> --
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
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