Re: [R] Making R talk to Win/OpenBUGS in Linux (again)

From: Uwe Ligges <ligges_at_statistik.uni-dortmund.de>
Date: Tue 02 May 2006 - 02:24:06 EST

Paul Johnson wrote:

> Thank you very much.  With the insertion of WINEPATH declaration, then
> the following example program does run.  And really fast, too!
> 
> 
> 
> 
> 
> library(R2WinBUGS)
> 
> WINEPATH <- "/usr/bin/winepath"


Will be fixed in the package real soon now. Gregor, many thanks for the patches.

Best,
Uwe Ligges

>                                         # An example model file is given in:
> model.file <- system.file(package = "R2WinBUGS", "model", "schools.txt")
> # Let's take a look:
> file.show(model.file)
> 
> # Some example data (see ?schools for details):
> data(schools)
> schools
> 
> J <- nrow(schools)
> y <- schools$estimate
> sigma.y <- schools$sd
> data <- list ("J", "y", "sigma.y")
> inits <- function(){
>     list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
>         sigma.theta = runif(1, 0, 100))
> }
> parameters <- c("theta", "mu.theta", "sigma.theta")
> 
> 
> schools.sim <- bugs(data, inits, parameters, model.file, n.chains = 3,
> n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/",
> working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T,
> WINE="/usr/bin/wine",WINEPATH=WINEPATH)
> 
> 
> 
> 
> On 4/30/06, Gregor Gorjanc <gregor.gorjanc@gmail.com> wrote:
> 

>>Hello Paul,
>>
>>thank you very much for this report. You caught a bug in R2WinBUGS that
>>was introduced by me. I added support for winepath in 1.1-1 version.
>>Since I switch between Windows and Linux I always set WINEPATH and then
>>use it in bugs(). That's why I forgot to add it in further calls in
>>bugs(). How silly :( This actually means that nobody else beside you
>>tried to run R2WinBUGS under Linux. To bad. Please report summary to
>>BUGS list as you have also asked there for help and I did not had time
>>to answer you. I have been successfully running R2WinBUGS under Linux
>>for quite some time now.
>>
>>Now you have the following options:
>>
>>A Set WINEPATH before you call bugs()
>>
>>i.e.
>>
>>WINEPATH <- "/usr/bin/winepath"
>>
>>bugs(..., WINEPATH=WINEPATH)
>>
>>This is the fastest approach for you.
>>
>>B Apply the following diffs, build and install R2WinBUGS by yourself
>>
>>I am also sendind them to maintainer of the package. So this should be
>>fixed soon also on CRAN. Uwe?
>>
>>--- R2WinBUGSOrig/R/bugs.R 2006-04-29 21:44:59.000000000 +0200
>>+++ R2WinBUGS/R/bugs.R 2006-04-30 12:52:36.000000000 +0200
>>@@ -44,7 +44,7 @@
>> } else new.model.file <- model.file
>> bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
>> bugs.directory, new.model.file, debug=debug, is.inits=!is.null(inits),
>>- bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE)
>>+ bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE,
>>WINEPATH=WINEPATH)
>> #if (useWINE && missing(bugs.directory))
>> # bugs.directory <- winedriveTr(bugs.directory)
>> bugs.run(n.burnin, bugs.directory, WINE = WINE)
>>
>>--- R2WinBUGSOrig/R/bugs.script.R 2006-04-29 21:44:59.000000000 +0200
>>+++ R2WinBUGS/R/bugs.script.R 2006-04-30 12:52:12.000000000 +0200
>>@@ -1,7 +1,7 @@
>> "bugs.script" <-
>> function (parameters.to.save, n.chains, n.iter, n.burnin,
>> n.thin, bugs.directory, model.file, debug=FALSE, is.inits, bin,
>>- DIC = FALSE, useWINE = FALSE, newWINE = FALSE){
>>+ DIC = FALSE, useWINE = FALSE, newWINE = FALSE, WINEPATH=NULL){
>>
>>
>>>I'm back!
>>>
>>>I've just learned that, on a fully updated Fedora Core Linux5 sytem,
>>>the working solution to access Winbugs under wine via the R package
>>>"rbugs" no longer works. Here was my last post on this topic (with
>>>the formerly working solution) from January.
>>>
>>>http://finzi.psych.upenn.edu/R/Rhelp02a/archive/68497.html
>>>
>>>Currently, what happens is that WinBUGS starts up, but just sits there
>>>doing nothing. I do not know if the problem is due to a change in
>>>wine or rbugs, and since both of them are updated, it is hard to say.
>>>I'm thinking it is a wine or perhaps even a kernel related problem.
>>>Inside WinBUGS running under wine, it does not even work to manually
>>>open the bugs.script file and then choose "Model/Script". it just
>>>returns a screen full of errors saying the commands fail. I don't
>>>think rbugs gets even that far, however, since the WinBUGS window does
>>>pop up, but nothing happens.
>>>
>>>rbugs has been retooled to emphasize use of linbugs, the
>>>OpenBUGS-based thing for linux, but I can't get linbugs to run at all
>>>on my system, and the linbugs program itself appears to have been
>>>removed from OpenBUGS distribution altogether. (I'm following that
>>>with separate email to the OpenBUGS group).
>>>
>>>I think JAGS is the right long term solution, but currently I'm in the
>>>middle of a semester trying to teach about Bayesian stats and the
>>>students have some familiarity with WinBUGS and I'm interested in
>>>making it work. So while I'm learning more about JAGS and the bayesmix
>>>package that supports access to it from R, I still would like a way to
>>>interact with Winbugs through Wine.
>>>
>>>If anybody has rbugs working in current Linux, please tell me
>>>how--give me a working example?
>>>
>>>In the meanwhile, I've noticed that nightly updates have successfully
>>>installed R2WinBUGS on linux systems and I've got a small test case
>>>that I'd like to ask about. Since rbugs is a linux adaptation of
>>>R2WinBUGS, and R2WinBUGS is now buildable on Linux, it looks like
>>>R2WinBUGS may be the way to go. But it fails. The error centers
>>>around the "WINEPATH" setting. I've learned that wine has a function
>>>"winepath" that returns information that programs can use, and I've
>>>fiddled this lots of ways, but it fails, saying
>>>
>>>
>>>Error in paste(WINEPATH, "-w", x) : object "WINEPATH" not found
>>>library(R2WinBUGS)
>>>
>>>I hope that by giving you this small not-yet-working example, you can
>>>spot where I'm going wrong.
>>>
>>>##Paul Johnson 2006-04-29
>>>
>>>
>>>library(R2WinBUGS)
>>># Copied from Prof Andrew Gelman's example
>>>model.file <- system.file(package = "R2WinBUGS", "model", "schools.txt")
>>>#
>>>file.show(model.file)
>>>data(schools)
>>>schools
>>>
>>>J <- nrow(schools)
>>>y <- schools$estimate
>>>sigma.y <- schools$sd
>>>data <- list ("J", "y", "sigma.y")
>>>inits <- function(){
>>> list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
>>> sigma.theta = runif(1, 0, 100))
>>>}
>>>parameters <- c("theta", "mu.theta", "sigma.theta")
>>>
>>>
>>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains = 3,
>>>n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/",
>>>working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T,
>>>WINE="/usr/bin/wine",WINEPATH="/usr/bin/winepath")
>>>
>>>
>>>
>>>I do have the binary "/usr/bin/winepath", but can't tell how to give
>>>R2WinBUGS what it wants. Many failed efforts below:
>>>
>>>
>>>
>>>
>>>>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains = 3, n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/", working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T, WINE="/usr/bin/wine",WINEPATH="/usr/bin/")
>>>
>>>Error in paste(WINEPATH, "-w", x) : object "WINEPATH" not found
>>>
>>>
>>>>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains = 3, n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/", working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T, WINE="/usr/bin/wine")
>>>
>>>Error in if (!nchar(WINEPATH)) { : argument is of length zero
>>>
>>>
>>>>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains = 3, n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/", working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T, WINE="/usr/bin/wine",WINEPATH="/usr/bin")
>>>
>>>Error in paste(WINEPATH, "-w", x) : object "WINEPATH" not found
>>>
>>>
>>>
>>>I know there are many unknowns here, but hope somebody has at least
>>>one working example that we can build on.
>>
>>
>>--
>>Lep pozdrav / With regards,
>> Gregor Gorjanc
>>
>>----------------------------------------------------------------------
>>University of Ljubljana PhD student
>>Biotechnical Faculty
>>Zootechnical Department URI: http://www.bfro.uni-lj.si/MR/ggorjan
>>Groblje 3 mail: gregor.gorjanc <at> bfro.uni-lj.si
>>
>>SI-1230 Domzale tel: +386 (0)1 72 17 861
>>Slovenia, Europe fax: +386 (0)1 72 17 888
>>
>>----------------------------------------------------------------------
>>"One must learn by doing the thing; for though you think you know it,
>> you have no certainty until you try." Sophocles ~ 450 B.C.
>>----------------------------------------------------------------------
>>
>>
>>
> 
> 
> 
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
> 
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