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

From: Manuel Morales <Manuel.A.Morales_at_williams.edu>
Date: Tue 02 May 2006 - 05:42:12 EST

As far as I can figure out, the problem with running "LinBUGS" on FC5 is that support for linuxthreads was removed after being deprecated in FC4.

http://fedora.redhat.com/docs/release-notes/fc5/#id2887615

As a result, the LD_ASSUME_KERNEL workaround, which presumably forced the use of linuxthreads (see
http://www.math.helsinki.fi/openbugs/phpBB2/viewtopic.php?t=4), doesn't work anymore.

Ideally, bugs.so / brugs.so would be compiled with support for NPTL instead of linuxthreads, but I don't think it's possible to do this as an end user. Unless changes are made by the OpenBUGS developers, OpenBUGS will not run natively in FC5.

Manuel

On Mon, 2006-05-01 at 13:38 -0500, Paul Johnson wrote:
> Dear Jun:
>
> How about telling us which version of Linux you use and how you make
> linbugs run? As far as I can tell, the OpenBUGS people have
> intentionally removed linbugs from their version 2.2. That leaves us
> with various scripts that people have posted & tried, none work for
> me. Fedora Core 5, I cannot get any of the linbugs scripts that are
> floating around to work.
>
> I tried re-building the program thus:
>
>
> # gcc -o cbugs CBugs.c -ldl
>
> That creates an executable cbugs, but there is no joy for me.
>
> $ ./cbugs
> failed to install signal
> 32
> failed to install signal
> 33
>
> ****
> * BlackBox
> * illegal memory read [ad = 00000000]
> - HostFiles.NewFileRef (pc=00000D9B, fp=BFC73BE4)
> - HostFiles.OpenFile (pc=00000E0E, fp=BFC73BFC)
> - HostFiles.Directory.Old (pc=000029B2, fp=BFC73EA4)
> - StdLoader.ThisObjFile (pc=0000031D, fp=BFC744C0)
> - StdLoader.ReadHeader (pc=0000075F, fp=BFC746E0)
> - StdLoader.LoadMod (pc=0000107B, fp=BFC747F8)
> - StdLoader.LoadMod (pc=000011E0, fp=BFC74910)
> - StdLoader.LoadMod (pc=000011E0, fp=BFC74A28)
> - StdLoader.Hook.ThisMod (pc=00001355, fp=BFC74A3C)
> - Kernel.ThisMod (pc=00001224, fp=BFC74B58)
> - Init.Init (pc=0000004B, fp=BFC74B70)
> - Init.$$ (pc=0000000A, fp=BFC74B80)
> ****
>
>
>
> # export LD_ASSUME_KERNEL=2.4.1
>
>
> # ./cbugs
> ./cbugs: error while loading shared libraries: libdl.so.2: cannot open
> shared object file: No such file or directory
>
> $ ldd ./cbugs
> linux-gate.so.1 => (0x00a2b000)
> libdl.so.2 => /lib/libdl.so.2 (0x00ba9000)
> libc.so.6 => /lib/libc.so.6 (0x00a4d000)
> /lib/ld-linux.so.2 (0x00a2c000)
>
> And after doing that LD_ASSUME_KERNEL thingie, nothing in the shell
> works anymore...
>
> $ which cbugs
> /usr/bin/which: error while loading shared libraries: libc.so.6:
> cannot open shared object file: No such file or directory
>
> On 5/1/06, jun yan <jyan@stat.uiowa.edu> wrote:
> > I have used linbugs with the rbugs package for a recent work. It might be
> > worthwhile trying.
> >
> > Jun
> >
> >
> >
> > On 5/1/06, Uwe Ligges <ligges@statistik.uni-dortmund.de>
> > wrote:
> > > 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
> > > >
> > > > ______________________________________________
> > > > R-help@stat.math.ethz.ch mailing list
> > > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > > PLEASE do read the posting guide!
> > http://www.R-project.org/posting-guide.html
> > >
> > > ______________________________________________
> > > R-help@stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide!
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> > >
> >
> >
>
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
>
> ______________________________________________
> R-help@stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html



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