[R] Current state of support for BUGS access for Linux users?

Paul Johnson pauljohn32 at gmail.com
Wed Jan 18 06:40:29 CET 2006

Thanks!  Let me ask this question again.  Clearly, if you experts
can't make R talk to WinBUGS, then I can't either.  So, If "bugs()"
doesn't work, What is the next best thing?

With wine, I can run OpenBUGS and WinBUGS, but I cannot send jobs from
R to a BUGS program (still trying, some people say they have seen
rbugs work in Linux).

I want to follow along with the instructions In Prof Gelman's site for
R2WinBUGS.  OR the examples in the rbugs package.  I just noticed that
rbugs works by writing the data, model, inits, and so forth into text
files, along with a script that drives WinBUGS.  Although there is
something wrong with the script file that causes a fatal WinBUGS
crash, I have just manually started the GUI and pointed and clicked my
way to a working set of  BUGS estimates (see details on script flaw
and trap below).

That makes me feel a bit confident that I will be able to create
working BUGS sims and get results.  I need to learn how to bring into
R from CODA output.  In the WinBUGS output, I find a codaIndex.txt
file that looks promising.

Now, about efforts to run WinBUGS from within R. In case other people
are trying this, here is what I learned.

1. bugs() from R2WinBUGS to WinBUGS14 under wine-0.9.5 is not able to
start WinBUGS14.exe

I've just tried the newest example from
http://www.stat.columbia.edu/~gelman/bugsR/ with WinBUGS14 under wine.

WinBUGS never shows on the screen before the error appears:

> library(R2WinBUGS)
> schools <- read.table ("schools.dat", header=T)
> 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,
+                      "schools.bug",
+                      bugs.directory = "/usr/local/share/WinBUGS14/",
+                      n.chains=3,
+                      n.iter=1000,
+                      useWINE= T,
+                      WINE = "/usr/bin/wine"
+                      )
Loading required package: tools
Error in pmatch(x, table, duplicates.ok) :
	argument is not of mode character


I tried running this under debug, but can't understand the output. I
get through about 8 steps, when bugs.script() seems to cause the
Browse[1]> n
debug: 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)
Browse[1]> n
Error in pmatch(x, table, duplicates.ok) :
	argument is not of mode character

2. With the "rbugs" package and WinBUGS14, I get a lot further.  From
fumbling around in this code, I can tell that rbugs writes text files
in the working directory and then tells WinBUGS to start and access
those files.  This code causes the WinBUGS GUI to pop up and it goes
pretty far. Using the exact same code as in the R2WinBUGS example
above, observe:

schools.sim <- rbugs ( data,
                      n.burnin = 1000, n.chains=1, n.iter=1000,

As I said, the WinBUGS14 window opens, the log file says

model is syntactically correct
data loaded
model compiled
model is initialized
command #Bugs:gen.inits cannot be executed (is greyed out)
no monitor set

However, after all that up pops a window called "TRAP"  (pasted next).
 I believe this is going wrong becuase the fourth-to-last line is
update(0).  If I manually change that to update(30000), then the
script does not crash.  So there's something wrong in rbugs in taking
"n.iter" into the script.  I'll try to follow that up.

Here's the TRAP window output.  I believe it is much ado about
nothing--update(0) is causing it.

undefined real result

 MonitorsSummary.StdMonitor.Mean   [000002FBH]
	.mean	REAL	2.121995790965272E-314
	.monitor	MonitorsSummary.StdMonitor	[0113F3F0H]
 DeviancePlugin.EstimatedMeans   [000003FBH]
	.cursor	GraphStochastic.List	[01145FE0H]
	.j	INTEGER	2143872776
	.list	GraphStochastic.List	[01145FE0H]
	.node	GraphStochastic.Node	[01044600H]
	.size	INTEGER	1
	.value	REAL	2.121995790965272E-314
 DevianceInterface.DICAll   [0000058EH]
	.dBar	REAL	3.486226116065809E+307
	.dBarTotal	REAL	3.486184325428448E+307
	.dHat	REAL	1.856490554558022E-303
	.dHatTotal	REAL	8.948601956767742E-317
	.dicTotal	REAL	1.342105535202697E-102
	.f	TextMappers.Formatter	Fields
	.i	INTEGER	2143868088
	.monitors	POINTER	[01145ED0H]
	.num	INTEGER	1
	.pDTotal	REAL	4.244199150914158E-313
	.res	INTEGER	0
 DevianceCmds.DIC   [0000012DH]
	.asc	INTEGER	104775
	.dsc	INTEGER	28575
	.f	TextMappers.Formatter	Fields
	.height	INTEGER	16821552
	.lines	INTEGER	553779732
	.res	INTEGER	0
	.t	TextModels.Model	[01145E50H]
	.title	ARRAY 256 OF CHAR	"DIC"
	.width	INTEGER	114300
 StdInterpreter.CallProc   [0000047AH]
	.i	Meta.Item	Fields
	.imported	ARRAY 256 OF CHAR	""   ...
	.importing	ARRAY 256 OF CHAR	""   ...
	.mn	Meta.Name	"DevianceCmds"
	.mod	StdInterpreter.Ident	"DevianceCmds"
	.object	ARRAY 256 OF CHAR	""   ...
	.parType	INTEGER	3
	.pn	Meta.Name	"DIC"
	.proc	StdInterpreter.Ident	"DIC"   ...
	.res	INTEGER	0
	.v	StdInterpreter.ProcVal	Fields
	.vi	StdInterpreter.ProcIVal	Fields
	.vii	StdInterpreter.ProcIIVal	Fields
	.vr	StdInterpreter.ProcRVal	Fields
	.vri	StdInterpreter.ProcRIVal	Fields
	.vrii	StdInterpreter.ProcRIIVal	Fields
	.vrr	StdInterpreter.ProcRRVal	Fields
	.vrri	StdInterpreter.ProcRRIVal	Fields
	.vrrii	StdInterpreter.ProcRRIIVal	Fields
	.vrs	StdInterpreter.ProcRSVal	Fields
	.vrsi	StdInterpreter.ProcRSIVal	Fields
	.vrsii	StdInterpreter.ProcRSIIVal	Fields
	.vs	StdInterpreter.ProcSVal	Fields
	.vsi	StdInterpreter.ProcSIVal	Fields
	.vsii	StdInterpreter.ProcSIIVal	Fields
	.vsr	StdInterpreter.ProcSRVal	Fields
	.vsri	StdInterpreter.ProcSRIVal	Fields
	.vsrii	StdInterpreter.ProcSRIIVal	Fields
	.vss	StdInterpreter.ProcSSVal	Fields
	.vssi	StdInterpreter.ProcSSIVal	Fields
	.vssii	StdInterpreter.ProcSSIIVal	Fields
 StdInterpreter.Command   [0000131CH]
	.left	StdInterpreter.Ident	"DevianceCmds"
	.ptype	INTEGER	3
	.right	StdInterpreter.Ident	"DIC"   ...
 StdInterpreter.CallHook.Call   [00001441H]
	.ch	CHAR	0X
	.e	ARRAY 64 OF CHAR	""   ...
	.errorMsg	ARRAY 1 OF CHAR	""
	.f	ARRAY 64 OF CHAR	""   ...
	.g	ARRAY 64 OF CHAR	""   ...
	.hook	StdInterpreter.CallHook	[01060050H]
	.i	INTEGER	24
	.i0	INTEGER	0
	.i1	INTEGER	0
	.id	StdInterpreter.Ident	"DIC"   ...
	.par0	Dialog.String	""   ...
	.par1	Views.Title	""   ...
	.proc	ARRAY 240 OF CHAR	"DevianceCmds.DIC('DIC')"   ...
	.res	INTEGER	0
	.s0	Dialog.String	"DIC"
	.s1	Dialog.String	""   ...
	.type	INTEGER	3
 Dialog.Call   [00002FC8H]
	.errorMsg	ARRAY 1 OF CHAR	""
	.proc	ARRAY 240 OF CHAR	"DevianceCmds.DIC('DIC')"   ...
	.res	INTEGER	0
 BugsScript.Call   [00000130H]
	.bugsCommands	ARRAY 240 OF CHAR	"DevianceCmds.DIC('DIC')"   ...
	.i	INTEGER	23
	.item	Meta.Item	Fields
	.j	INTEGER	23
	.par	Dialog.Par	Fields
	.pos	INTEGER	-1
	.res	INTEGER	0
	.s	ARRAY 240 OF CHAR	"DevianceCmds.DIC('DIC')"   ...
	.scriptCommand	ARRAY 240 OF CHAR	"#Bugs:dic.stats"   ...
	.start	INTEGER	18
	.v	BugsScript.RECORD	Fields
 BugsScript.Action.Do   [0000062FH]
	.a	BugsScript.Action	[011D2120H]
	.argNum	INTEGER	0
	.bugsCommands	ARRAY 240 OF CHAR	"DevianceCmds.DIC('DIC')"   ...
	.p	ARRAY 3, 120 OF CHAR	Elements
	.s	BugsScanners.Scanner	Fields
	.scriptCommand	ARRAY 240 OF CHAR	"#Bugs:dic.stats"   ...
	.vectorName	BOOLEAN	FALSE
 Services.Exec   [00000136H]
	.a	Services.Action	[011D2120H]
	.t	POINTER	[21C90170H]
 Services.IterateOverActions   [000002F4H]
	.p	Services.Action	[011D2120H]
	.time	LONGINT	3498
 Services.StdHook.Step   [0000034DH]
	.h	Services.StdHook	[0101E380H]
 HostWindows.Idle   [00004A86H]
	.tick	Controllers.TickMsg	Fields
	.w	HostWindows.Window	NIL
 HostMenus.TimerTick   [00003422H]
	.lParam	INTEGER	0
	.ops	Controllers.PollOpsMsg	Fields
	.wParam	INTEGER	1
	.wnd	INTEGER	65574
 Kernel.Try   [00003A61H]
	.a	INTEGER	65574
	.h	PROCEDURE	HostMenus.TimerTick
 HostMenus.ApplWinHandler   [00003841H]
	.hit	BOOLEAN	Undefined70
	.lParam	INTEGER	0
	.message	INTEGER	275
	.res	INTEGER	1180843108
	.s	ARRAY 256 OF SHORTCHAR	2X   ...
	.w	INTEGER	538416909
	.wParam	INTEGER	1
	.wnd	INTEGER	65574
<system>   (pc=465EDB29H,  fp=7FC8FB00H)
<system>   (pc=465EE418H,  fp=7FC8FB3CH)
<system>   (pc=465F1DF0H,  fp=7FC8FB80H)
<system>   (pc=465BD031H,  fp=7FC8FBB0H)
 HostMenus.Loop   [00003BDEH]
	.f	SET	{0..5}
	.res	INTEGER	0
	.w	HostWindows.Window	NIL
 Kernel.Start   [00002B8CH]
	.code	PROCEDURE	HostMenus.Loop

3. Accessing OpenBUGS with wine from "rbugs" gets as far as opening
the OpenBUGS GUI, but nothing ever appears in the log file and there
are no computations going on (according to system monitors, anyway),
but everything in OpenBUGS just seems stuck.


On 1/17/06, Uwe Ligges <ligges at statistik.uni-dortmund.de> wrote:
> Paul Johnson wrote:
> > Thanks, Uwe
> >
> > that clears up why I can't make R2WinBUGs work with OpenBUGS and WinBUGS1.5 :)
> > Both work pretty good with Wine in a GUI.  I noticed that when I tried
> > "rbugs", it does succeed in starting WinBUGS GUI, but then nothing
> > happens. I'll get WinBUGS1.4 and see what happens.
> >
> > In the meanwhile, I'm going to t ry to see what BRugs is good for. In
> > Linux, when I try to install BRugs, the install fails with an error
> > saying that, at the current time, BRugs works only in Windows.
> Yes, I have added that particular line in order not to confuse users,
> and I thought I told you in my last message that it works only under
> Windows.
> > * Installing *source* package 'BRugs' ...
> > Package 'BRugs' currently only works under Windows.\nIt is supposed to
> > work under Linux in future releases.
> >
> > I'd like to stop that check and see what happens!
> OK, just remove the configure file.
> > The way I read the
> > sourcecode from OpenBUGS and BRugs, I need to replace the windows dll
> > install and instead put in an so file (as in OpenBUGS).
> Yes, it is already shipped, and the infrastructure in the package is
> ready (hopefully), but the brugs.so file does not work as expected.
> > If anybody has done this, please let me know of your experience.
> Yes, several tried, among them Andrew Thomas and Uwe Ligges, and then I
> invited Andrew Thomas to Dortmund and we tried together (I have to admit
> that I was clueless all the time and in fact Andrew tried).
> Andrew's conclusion was that there is some compiler problem on Linux
> with the BlackBox framework (Component Pascal compiler from Oberon
> microsystems) in which WinBUGS/OpenBUGS is written in ...
> If you get it to work, please let us know!
> Uwe

Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

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