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How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009

10 messages · Uwe Ligges, chaogai, Tobias Verbeke +1 more

Paul Heinrich Dietrich
# 
Hi all,
I've managed to get JAGS working on my Ubuntu Hardy Linux with a 32-bit
computer and AMD processors using R 2.8.1.  JAGS is great.  I've read that
JAGS is the fastest, but that hasn't been my experience.  At any rate, I
have more experience with WinBUGS under Windows and would like a version of
that working as well.

It seems like I've read a lot on the subject and tried a lot, but haven't
managed to get BUGS to work yet.  The most success I've had is to install
WinBUGS or OpenBUGS using this method:
http://www.math.aau.dk/~slb/kurser/bayes-08/install.html

What you also need to know is that you need to open Wine and add a drive. 
Although Z is recommended, I haven't been able to specify it, but have
gotten a D drive to work, using:

wine D:/opt/OpenBUGS/winbugs.exe

Using this method, OpenBUGS opens.  Now, to be able to open it with R.  I've
read all sorts of discussions about BRugs (which is no longer on CRAN, but
old versions can still be found), rbugs, and R2WinBUGS (which I'm used to
using on Windows with WinBUGS).  Some people say R2WinBUGS cannot run
OpenBUGS on Linux, some claim they've done it (I think).  It seems the same
thing with everything else.  I've tried making the linbugs and cbugs file
recommended elsewhere online.  It's all very confusing.

Can someone show a method that works currently, along with some sample code? 
I'm also new to Linux, and confused by path conventions.  For example, in
rbugs, it shows an example of a path such as
"/var/scratch/jyan/wine-20040408/wine", and I don't see how to modify this. 
I have no /var/scratch to begin with, and think Wine is installed in
/home/me/.wine...(I don't have Linux in front of me right now).

Please help.  Thanks.
Uwe Ligges
#
Paul Heinrich Dietrich wrote:
For short: It is quite unlikely that BRugs / OpenBUGS (which is called 
LinBUGS under Linux) works natively under your Linux (although it might 
work under very specific settings). BRugs is available for Windows users 
from the "CRAN extras" repsository maintained by Brian Ripley. We moved 
it in order to meet GPL compliance issues.

Hence a standard recommendation is to use R2WinBUGS under native R under 
Linux with WinBUGS running under wine. R2WinBUGS can use wine to do so. 
See the help page ?bugs once you have loaded R2WinBUGS.

Best wishes,
Uwe Ligges
Paul Heinrich Dietrich
# 
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.
chaogai
# 
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:

            

      
      
      
    

        
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      Tobias Verbeke
    

    

      
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Uwe Ligges wrote:

        

            

      
      
      
    

        
As every now and then I get offline requests from people who stumble on 
this thread

http://finzi.psych.upenn.edu/R/Rhelp08/archive/132855.html

to give details on how I got OpenBUGS running under GNU/Linux,
I made a stripped-down package that does just that. The approach is 
very, very basic and I only tested this on a few machines and
distributions, but if it can be useful to anyone, I temporarily
put it up at

http://www.openanalytics.be/rOpenBUGS_0.0-1.tar.gz

Best,
Tobias

  
  


  


      

    

    

      
      

        


  

        

      Paul Heinrich Dietrich
    

    

      
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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:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Paul Heinrich Dietrich
    

    

      
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Tobias, this looks great!  I'm new to Linux, and I've only installed packages
from within R with install.packages().  I'm guessing that I should unzip
ROpenBUGS to the following path:

/usr/local/lib/R/site-library/

...just checking because I'm new and don't want to do it wrong.  Thanks.

PS
This really looks great.  Any thought to making this a permanently available
package on CRAN?

        
Tobias Verbeke-4 wrote:

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      chaogai
    

    

      
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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:

        

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
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      Paul Heinrich Dietrich
    

    

      
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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:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    
1 day later

    

      
      

        


  

        

      Paul Heinrich Dietrich
    

    

      
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I just wanted to post in conclusion to this threat that I have had success
running WinBUGS from R via R2WinBUGS, with the help of Gorjanc, Uwe, and Ben
by email outside of this thread.

I may have had a permissions problem, that was probably corrected by
entering this in the terminal:

me at computer:~$ chmod -R u+w /home/me/.wine/drive_c/"Program
Files"/WinBUGS14/

            

      
      
      
    

        
copy/pasted the example, and ran it exactly.

My mistake that prevented it all from running was that I started R as sudo
R, thinking that would give me more permissions, because I thought I was
having permissions-oriented problems.  But this is wrong.  When I started R
by merely entering R in the terminal, the example code ran perfectly. 
Success!  Winepaths did not have to be specified because WinBUGS was
installed in the usual place (c:/Program Files/WinBUGS14/").

Other people have emailed me, indicating that newer versions of WINE have
not worked for them, so I am back with WINE 1.0.  I hope this helps others
trying to run WinBUGS on Linux.