bugs-r-devel Mailing List for BUGS-R (Page 22)

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Ben Bolker wrote:
> Gregor Gorjanc wrote:
>> Hello Ben!
>>
>> Sorry for late reply. I am swamped with my work. Anyway.
>>
>> I (with Uwe) have setup SourceForge BUGS-R[1] project for packages like
>> R2WinBUGS and BRugs. I am very interested in your chnages and would like
>> to ask you if you can create diffs against latest version in SVN and
>> send them so I can check. Sorry for being a bit lazy ;)
>>
>> Thanks!
>>
>> Gregor
>>
>> [1]http://sourceforge.net/projects/bugs-r/
>>
> 
>   this time it's my fault for the delay.
> 
>   Here are my diffs against today's trunk ...
> 
>   cheers
>     Ben
> 
> 
> 
> ------------------------------------------------------------------------
> 
> *** bugs.R	2006-10-08 13:59:48.000000000 -0400
> --- /home/ben/bugs-r/trunk/R2WinBUGS/R/bugs.R	2006-12-10 16:21:31.000000000 -0500
> ***************
> *** 8,14 ****
>       program = c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
>       working.directory = NULL,
>       clearWD = FALSE, useWINE = .Platform$OS.type != "windows", WINE = Sys.getenv("WINE"),
> !     newWINE = FALSE, WINEPATH = Sys.getenv("WINEPATH")){
>       
>     ## If OpenBUGS, we only call openbugs() and exit...
>     program <- match.arg(program)
> --- 8,14 ----
>       program = c("winbugs", "openbugs", "WinBugs", "OpenBugs"),
>       working.directory = NULL,
>       clearWD = FALSE, useWINE = .Platform$OS.type != "windows", WINE = Sys.getenv("WINE"),
> !     newWINE = FALSE, WINEPATH = NULL){
>       
>     ## If OpenBUGS, we only call openbugs() and exit...
>     program <- match.arg(program)
> ***************
> *** 54,60 ****
>     bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
>       new.model.file, debug=debug, is.inits=!is.null(inits),
>       bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE, WINEPATH = WINEPATH)
> !   bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE, WINEPATH=WINEPATH)
>   
>     if(codaPkg)
>       return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
> --- 54,60 ----
>     bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
>       new.model.file, debug=debug, is.inits=!is.null(inits),
>       bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE, WINEPATH = WINEPATH)
> !   bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE = useWINE)
>   
>     if(codaPkg)
>       return(file.path(getwd(), paste("coda", 1:n.chains, ".txt", sep="")))
> 
> 
> ------------------------------------------------------------------------
> 
> *** bugs.run.R	2006-10-08 14:18:03.000000000 -0400
> --- /home/ben/bugs-r/trunk/R2WinBUGS/R/bugs.run.R	2006-12-10 16:21:31.000000000 -0500
> ***************
> *** 1,12 ****
>   "bugs.run" <-
>       function(n.burnin, bugs.directory, WINE = "", 
> !              useWINE = .Platform$OS.type != "windows", newWINE = TRUE,
> !              WINEPATH=Sys.getenv("WINEPATH")){
> ! 
> !       ## BMB: why should this have worked (without translating bugs.directory)
> !       ## if newWINE=TRUE ??
> !       if(useWINE) bugs.directory <- win2native(bugs.directory,WINEPATH=WINEPATH)
>   
>   
>   ## Update the lengths of the adaptive phases in the Bugs updaters
>     try(bugs.update.settings(n.burnin, bugs.directory))
> --- 1,8 ----
>   "bugs.run" <-
>       function(n.burnin, bugs.directory, WINE = "", 
> !              useWINE = .Platform$OS.type != "windows", newWINE = TRUE){
>   
> + if(useWINE && !newWINE) bugs.directory <- win2native(bugs.directory)
>   
>   ## Update the lengths of the adaptive phases in the Bugs updaters
>     try(bugs.update.settings(n.burnin, bugs.directory))
> ***************
> *** 21,28 ****
>       stop(paste("WinBUGS executable does not exist in", bugs.directory))
>   ## Call Bugs and have it run with script.txt
>     bugsCall <- paste("\"", dos.location, "\" /par \"",
> !                     native2win(file.path(getwd(), "script.txt"), newWINE = newWINE,
> !                                WINEPATH=WINEPATH),
>                       "\"", sep = "")
>     if (useWINE)
>       bugsCall <- paste(WINE, bugsCall)
> --- 17,23 ----
>       stop(paste("WinBUGS executable does not exist in", bugs.directory))
>   ## Call Bugs and have it run with script.txt
>     bugsCall <- paste("\"", dos.location, "\" /par \"",
> !                     native2win(file.path(getwd(), "script.txt"), newWINE = newWINE),
>                       "\"", sep = "")
>     if (useWINE)
>       bugsCall <- paste(WINE, bugsCall)
> 
> 
> ------------------------------------------------------------------------
> 
> *** bugs.script.R	2006-10-08 13:45:48.000000000 -0400
> --- /home/ben/bugs-r/trunk/R2WinBUGS/R/bugs.script.R	2006-12-10 16:21:31.000000000 -0500
> ***************
> *** 17,31 ****
>     coda  <- file.path(working.directory, "coda")
>     logfile <- file.path(working.directory, "log.odc")
>     logfileTxt <- file.path(working.directory, "log.txt")
> !   inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""),
> !                   native2win,WINEPATH=WINEPATH)
>     initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
>     savelist <- paste("set (", parameters.to.save, ")\n", sep="")
>     redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
>     cat(
>       "display ('log')\n",
> !     "check ('", native2win(model,WINEPATH=WINEPATH), "')\n",
> !     "data ('", native2win(data,WINEPATH=WINEPATH), "')\n",
>       "compile (", n.chains, ")\n",
>       if(is.inits) initlist,
>       "gen.inits()\n",
> --- 17,30 ----
>     coda  <- file.path(working.directory, "coda")
>     logfile <- file.path(working.directory, "log.odc")
>     logfileTxt <- file.path(working.directory, "log.txt")
> !   inits <- sapply(paste(working.directory, "/inits", 1:n.chains, ".txt", sep=""), native2win)
>     initlist <- paste("inits (", 1:n.chains, ", '", inits, "')\n", sep="")
>     savelist <- paste("set (", parameters.to.save, ")\n", sep="")
>     redo <- ceiling((n.iter-n.burnin)/(n.thin*bin))
>     cat(
>       "display ('log')\n",
> !     "check ('", native2win(model), "')\n",
> !     "data ('", native2win(data), "')\n",
>       "compile (", n.chains, ")\n",
>       if(is.inits) initlist,
>       "gen.inits()\n",
> ***************
> *** 35,46 ****
>       if(DIC) "dic.set()\n",
>       rep(
>       c("update (", formatC(ceiling(bin), format = "d"), ")\n",
> !     "coda (*, '", native2win(coda,WINEPATH=WINEPATH), "')\n"),redo),
>       "stats (*)\n",
>       if(DIC) "dic.stats()\n",
> !     "history (*, '", native2win(history,WINEPATH=WINEPATH), "')\n",
> !     "save ('", native2win(logfile,WINEPATH=WINEPATH), "')\n", 
> !     "save ('", native2win(logfileTxt,WINEPATH=WINEPATH), "')\n",
>       file=script, sep="", append=FALSE)
>     if (!debug) cat ("quit ()\n", file=script, append=TRUE)
>     sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
> --- 34,45 ----
>       if(DIC) "dic.set()\n",
>       rep(
>       c("update (", formatC(ceiling(bin), format = "d"), ")\n",
> !     "coda (*, '", native2win(coda), "')\n"),redo),
>       "stats (*)\n",
>       if(DIC) "dic.stats()\n",
> !     "history (*, '", native2win(history), "')\n",
> !     "save ('", native2win(logfile), "')\n", 
> !     "save ('", native2win(logfileTxt), "')\n",
>       file=script, sep="", append=FALSE)
>     if (!debug) cat ("quit ()\n", file=script, append=TRUE)
>     sims.files <- paste ("coda", 1:n.chains, ".txt", sep="")
> 
> 
> ------------------------------------------------------------------------
> 
> *** wineutils.R	2006-10-08 14:07:50.000000000 -0400
> --- /home/ben/bugs-r/trunk/R2WinBUGS/R/wineutils.R	2006-12-10 16:21:31.000000000 -0500
> ***************
> *** 43,58 ****
>   }
>   
>   
> ! win2native <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE,
> !                        WINEPATH=Sys.getenv("WINEPATH")) { # win -> native
> !   if (useWINE && !newWINE) winedriveTr(x)
> !   if (useWINE && newWINE) {
> !     system(paste(WINEPATH,' \"',x,'\"',sep=""), intern=TRUE)
> !   } else x
>   }
>   
> ! native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE,
> !                        WINEPATH=Sys.getenv("WINEPATH")) { # native -> win
>     if (useWINE && !newWINE) return(winedriveRTr(x))
>     if (useWINE && newWINE) {
>         x <- system(paste(WINEPATH, "-w", x), intern = TRUE)
> --- 43,54 ----
>   }
>   
>   
> ! win2native <- function(x, useWINE=.Platform$OS.type != "windows") { # win -> native
> !   if (useWINE) winedriveTr(x)
> !   else x
>   }
>   
> ! native2win <- function(x, useWINE=.Platform$OS.type != "windows", newWINE=TRUE) { # native -> win
>     if (useWINE && !newWINE) return(winedriveRTr(x))
>     if (useWINE && newWINE) {
>         x <- system(paste(WINEPATH, "-w", x), intern = TRUE)

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