R/mem.R

In BioStaCs/BSCgas: Greedy AUC stepwise

# The original posthttp://stackoverflow.com/questions/1395270/determining-memory-usage-of-objects
# As it is not in any package, we record it here.
# improved list of objects
# .ls.objects: Dirk Eddelbuettel
.ls.objects <- function (pos = 1, pattern, order.by,
                         decreasing=FALSE, head=FALSE, n=5) {
  napply <- function(names, fn) sapply(names, function(x)
    fn(get(x, pos = pos)))
  names <- ls(pos = pos, pattern = pattern)
  obj.class <- napply(names, function(x) as.character(class(x))[1])
  obj.mode <- napply(names, mode)
  obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
  obj.prettysize <- napply(names, function(x) {
    capture.output(print(object.size(x), units = "auto")) })
  obj.size <- napply(names, object.size)
  obj.dim <- t(napply(names, function(x)
    as.numeric(dim(x))[1:2]))
  vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
  obj.dim[vec, 1] <- napply(names, length)[vec]
  out <- data.frame(obj.type, obj.size, obj.prettysize, obj.dim)
  names(out) <- c("Type", "Size", "PrettySize", "Rows", "Columns")
  if (!missing(order.by))
    out <- out[order(out[[order.by]], decreasing=decreasing), ]
  if (head)
    out <- head(out, n)
  out
}

# shorthand
lsos <- function(..., n=10) {
  .ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

##showMemoryUse:  Michael Hallquist
showMemoryUse <- function(sort="size", decreasing=FALSE, limit) {
  
  objectList <- ls(parent.frame())
  
  oneKB <- 1024
  oneMB <- 1048576
  oneGB <- 1073741824
  
  memoryUse <- sapply(objectList, function(x) as.numeric(object.size(eval(parse(text=x)))))
  
  memListing <- sapply(memoryUse, function(size) {
    if (size >= oneGB) return(paste(round(size/oneGB,2), "GB"))
    else if (size >= oneMB) return(paste(round(size/oneMB,2), "MB"))
    else if (size >= oneKB) return(paste(round(size/oneKB,2), "kB"))
    else return(paste(size, "bytes"))
  })
  
  memListing <- data.frame(objectName=names(memListing),memorySize=memListing,row.names=NULL)
  
  if (sort=="alphabetical") memListing <- memListing[order(memListing$objectName,decreasing=decreasing),] 
  else memListing <- memListing[order(memoryUse,decreasing=decreasing),] #will run if sort not specified or "size"
  
  if(!missing(limit)) memListing <- memListing[1:limit,]
  gc();
  print(memListing, row.names=FALSE)
  return(invisible(memListing))
}