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

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.
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Paul Heinrich Dietrich wrote:
> 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.
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

> 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.

I just wanted to post in conclusion to this thread 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/
>From here, I opened R, entered library(R2WinBUGS), then ?bugs, then
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.
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