transferLibrary.R

# Used to transfer all installed packages from one system to another.  
#  Note:  Systems must have similar OS's.   eg: cannot go from OS X to Ubuntu 


# These two functions are implementations of @DWin's suggestions on StackOverflow
#  http://stackoverflow.com/questions/7133394/migrating-r-libraries

txrL.Out <- transferLibrary.Out <- function(dir="~/git/misc/!SysAdmin", fileName="pkglist.Rdata", createIfMissing=TRUE, dx=TRUE) {
# depends on as.path()
#
# Arguments:  dx: use dropbox dir
  
  if (dx)
    dir <- "~/Dropbox/tmp" 

  dir <- path.expand(dir)

  # Check that dir exists
  if (createIfMissing) {    
    dir.create(dir, showWarnings=FALSE)
  }  else {
    if (!file.exists(dir))
      stop(dir, " NOT FOUND")
  }
 
  # in installed.packages(), the Priority column alludes to which packages come installed. 
  # Therefore, we want those with no specified priority. 
  # .... I"m not positive that this is true.  
  # We might be better off excluding priorities c("base", "recommended") 
  #   as I'm not sure if there are other ways for a package to have a different priority


  # Note: the name of object `save.pkg.list` must match with that of `transferLibrary.In`
  save.pkg.list <- installed.packages()[is.na(installed.packages()[ , "Priority"]), 1]
  save(save.pkg.list, file=as.path(dir, fileName))
}


txrL.In <-  transferLibrary.In <- function(dir="~/git/misc/!SysAdmin", fileName="pkglist.Rdata", dep=FALSE, update=TRUE, dx=TRUE) {
# depends on as.path()
# 
# Arguments:   dep:  If TRUE will also install dependencies. 
#           update:  If TRUE will run update.packages() after installation completes.
#               dx:  If TRUE will over-right the value in dir with a dropbox dir.

  if (dx)
    dir <- "~/Dropbox/tmp" 

  file <- as.path(dir, fileName)

  # Check that file exists
  if (!file.exists(file))
      stop(dir, " NOT FOUND")
  
  # load in the list of packages
  load(as.path(dir, "pkglist.Rdata"))

  # Install the packages
  # Note: the name of object `save.pkg.list` must match with that of `transferLibrary.Out`  
  install.packages(save.pkg.list, dependencies=dep)

  # update all packages, if flagged (TRUE by default)
  if (update)
    update.packages(checkBuilt=TRUE)
}

  # ------------------------------------------------------------------------------------ #


##   as.path  is maintained in the `utilsRS.r` file
##    copy+pasted here on 5/7/2013 
as.path <- function(..., ext="", fsep=.Platform$file.sep, expand=TRUE) {
# concatenates the `...` into a valid path, accounting for extra slashes and dot-dot's

  dots <- list(...)

  dots <- dots[!sapply(dots, is.null)]

  ## If first argument starts with "http" or "ftp" then fsep should be "/", unless specified otherwise
  if(any(grepl("^(http|ftp)", as.character(dots[[1]]))) && missing(fsep))
    fsep <- "/"

  # error check
  if (any(grepl("^/~", dots[[1]])))
    stop ("Path cannot start with `/~`\nDid you mean to just use `~` ?")

  ## If starts with fsep, we will preserve it.
  startWith <- ifelse(substr(dots[[1]], 1, 1) == fsep, fsep, "")
  
  # Clean up the input (removing superfluous slashes, dots, etc)
  cleaned <- lapply(dots, function(x) {      
                # remove any leading slashes
                x <- ifelse(substr(x, 1, 1) == fsep, substr(x, 2, nchar(x)), x) 
                
                # remove any trailing slashes
                lng <- nchar(x)
                x <- ifelse(substr(x, lng, lng) == fsep, substr(x, 1, lng-1), x) 

                # return x to cleaned
                x
              })

  cleaned[!sapply(cleaned, function(x) identical(nchar(x), integer(0)))]

  # put back any starting fsep
  cleaned[[1]] <- paste0(startWith,cleaned[[1]])

  # append '.ext' to last item
  if (!ext=="")
    cleaned[[length(cleaned)]] <- paste0(cleaned[[length(cleaned)]], ".", gsub("^\\.", "", ext))

  # checking for '..'   ie:  "~/git/" +  "../out" =>  "~/out"
  if(any (  grepl("\\.\\.", cleaned) )) {
    return(cleanDotDotPath, fsep=fsep, expand=expand)
  }

  # else
  putTogether <- do.call(file.path, c(cleaned, fsep=fsep))

  if (!expand)
      return(putTogether)
  return(path.expand(putTogether))
}