"bugs.update.settings" <-
  function (n.burnin, bugs.directory)
{
  char.burnin <- as.character(n.burnin - 1)
  if(is.R()) {
    .fileCopy <- file.copy
  } else {
    .fileCopy <- splus.file.copy
  }
  .fileCopy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
            file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),
            overwrite=TRUE)
  registry <- readBin(file.path(bugs.directory, "System/Rsrc/Registry.odc"),
                      "character", 400, size=1, endian="little")
  locale <- Sys.getlocale("LC_CTYPE")
  Sys.setlocale("LC_CTYPE", "C")
  if(is.R()) {
    info <- registry[regexpr("Int", registry, fixed=TRUE, useBytes=TRUE) > 0]
  } else {
    info <- registry[regexpr("Int", registry, fixed=TRUE) > 0]
  }
  while(regexpr("\r", info) > 0) {
    newline <- regexpr("\r", info)
    info <- substring(info, newline + 1)
    line <- substring(info, 1, regexpr("\r", info) - 1)
    if(regexpr("AdaptivePhase", line) > 0) {
      if(is.R()) {
        numpos <- regexpr("Int", line, fixed=TRUE, useBytes=TRUE) + 4
      } else {
        numpos <- regexpr("Int", line, fixed=TRUE) + 4
      }
      num <- substring(line, numpos)
      if(as.numeric(num) > n.burnin) {
        blanks <- rep(" ", nchar(num, type="chars") - nchar(char.burnin, type="chars"))
        num.new <- paste(paste(blanks, collapse=""), char.burnin, sep="")
        line.new <- sub(num, num.new, line)
        registry <- sub(line, line.new, registry)
      }
    }
  }
  Sys.setlocale("LC_CTYPE", locale)
  writeBin(registry,
           file.path(bugs.directory, "System/Rsrc/Registry.odc"), endian="little")
}

## TODO: why is not this function called just file.copy within !is.R()

"splus.file.copy"<-
  function(from, to, overwrite=FALSE)
{
  if(!file.exists(from))
    stop("File: ", from, " does not exist")
  if(!overwrite && file.exists(to))
    stop("File: ", to, " already exists and overwrite is FALSE")
  n <- file.info(from)$size
  z <- writeBin(readBin(from, what="integer", size=1, n=n), to, size=1)
  invisible(z)
}