I'm running into memory issues trying to plot a region from a .BAM file produced from RACE-seq. The .BAM file is not huge, but the high coverage might be the problem. Here's an example:

# Reproducing the memory problem
# First, source this alternative bam-file import function for use with Gviz::AlignmentsTrack. It will import a bamfile
# with non-UCSC chromosome names (i.e. "chr7" instead of just "7").
importFunctionNonUCSC <- function (file, selection) {
  indNames <- c(sub("\\.bam$", ".bai", file), paste(file, "bai", sep = "."))
  index <- NULL
  for (i in indNames) {
    if (file.exists(i)) {
      index <- i
      break
    }
  }
  if (is.null(index))
    stop("Unable to find index for BAM file '", file, "'. You can build an index using the following command:\n\t",
         "library(Rsamtools)\n\tindexBam(\"", file, "\")")
  pairedEnd <- parent.env(environment())[["._isPaired"]]
  if (is.null(pairedEnd))
    pairedEnd <- TRUE
  bf <- Rsamtools::BamFile(file, index = index, asMates = pairedEnd)
  # Rename chromosome names from UCSD to non-UCSC
  GenomeInfoDb::seqlevels(selection) <- sub(
    "chr",
    "",
    GenomeInfoDb::seqlevels(selection))
  param <- Rsamtools::ScanBamParam(
    which = selection,
    what = Rsamtools::scanBamWhat(),
    tag = "MD",
    flag = Rsamtools::scanBamFlag(isUnmappedQuery = FALSE))
  reads <- if (as.character(seqnames(selection)[1]) %in% names(Rsamtools::scanBamHeader(bf)$targets))
    Rsamtools::scanBam(bf, param = param)[[1]]
  else list()
  md <- if (is.null(reads$tag$MD))
    rep(as.character(NA), length(reads$pos))
  else reads$tag$MD
  if (length(reads$pos)) {
    layed_seq <- GenomicAlignments::sequenceLayer(reads$seq, reads$cigar)
    region <- unlist(Rsamtools::bamWhich(param), use.names = FALSE)
    ans <- stackStrings(
      layed_seq,
      start(region),
      end(region),
      shift = reads$pos - 1L,
      Lpadding.letter = "+",
      Rpadding.letter = "+")
    names(ans) <- seq_along(reads$qname)
  } else {
    ans <- DNAStringSet()
  }
  return(GRanges(
    # Return chromosome name prefixed with "chr"
    seqnames = if (is.null(reads$rname)) character() else paste("chr", reads$rname, sep=""),
    strand = if (is.null(reads$strand)) character() else reads$strand,
    ranges = IRanges(start = reads$pos, width = reads$qwidth),
    id = reads$qname, cigar = reads$cigar, mapq = reads$mapq,
    flag = reads$flag, md = md, seq = ans, isize = reads$isize,
    groupid = if (pairedEnd) reads$groupid else seq_along(reads$pos),
    status = if (pairedEnd) reads$mate_status else rep(factor("unmated", levels = c("mated", "ambiguous", "unmated")), length(reads$pos))))
}

# Create the alignments track
alTrack <- Gviz::AlignmentsTrack(
  range = "ETV1_cut_new.bam",
  isPaired = TRUE,
  genome = "hg19",
  name = "RNA coverage",
  ylim = c(0,1000),
  importFunction = importFunctionNonUCSC)

# Try to plot. More and more memory will be used until the program freezes and the only way out is to shut it down.
Gviz::plotTracks(
  alTrack,
  from = 13978871-50000,
  to = 13978871+50000,
  chromosome = "chr7")

I have not gotten any specific error messages myself, but a college got this:

## Warning in .Call2("XStringSet_xscat", args, PACKAGE = "Biostrings"):
## Reached total allocation of 8075Mb: see help(memory.size)

Which says that the problem might be in Biostrings. Can anyone here help me look into this? The .BAM file used in the example above can be downloaded here, and the .BAI file can be downloaded here.