copySubstitute {Biobase}R Documentation

Copy Between Connections or Files with Configure-Like Name-Value Substitution


Copy files, directory trees or between connections and replace all occurences of a symbol by the corresponding value.


copySubstitute(src, dest, symbolValues, symbolDelimiter="@", allowUnresolvedSymbols=FALSE, recursive = FALSE, removeExtension = "\.in$")


src Source, either a character vector with filenames and/or directory names, or a connection object.
dest Destination, either a character vector of length 1 with the name of an existing, writeable directory, or a connection object. The class of the dest argument must match that of the src argument.
symbolValues A named list of character strings.
symbolDelimiter A character string of length one with a single character in it.
allowUnresolvedSymbols Logical. If FALSE, then the function will execute stop if it comes across symbols that are not defined in symbolValues.
recursive Logical. If TRUE, the function works recursively down a directory tree (see details).
removeExtension Character. Matches to this regular expression are removed from filenames and directory names.


Symbol substitution: this is best explained with an example. If the list symbolValues contains an element with name FOO and value bar, and symbolDelimiter is @, then any occurence of @FOO@ is replaced by bar. This applies both the text contents of the files in src as well as to the filenames. See examples.

If recursive is FALSE, both src and dest must be connection or a filenames. The text in src is read through the function readLines, symbols are replaced by their values, and the result is written to dest through the function writeLines.

If recursive is TRUE, copySubstitute works recursively down a directory tree (see details and example). src must be a character vector with multiple filenames or directory names, dest a directory name.

One use of this function is in createPackage for the automatic generation of packages from a template package directory.


None. The function is called for its side effect.


Wolfgang Huber


## create an example file
infile  = tempfile()
outfile = tempfile()

writeLines(text=c("We will perform in @WHAT@:",
  "So, thanks to @WHOM@ at once and to each one,",
  "Whom we invite to see us crown'd at @WHERE@."),
  con = infile)

## create the symbol table
z = list(WHAT="measure, time and place", WHOM="all", WHERE="Scone")

## run copySubstitute
copySubstitute(infile, outfile, z)

## display the results

## This is a slightly more complicated example that demonstrates
## how copySubstitute works on nested directories
d = tempdir()
my.dir.create = function(x) {dir.create(x); return(x)}

unlink(file.path(d, "src"), recursive=TRUE)
unlink(file.path(d, "dest"), recursive=TRUE)

## create some directories and files:
src  = my.dir.create(file.path(d, "src"))
dest = file.path(d, "dest")
d1   = my.dir.create(file.path(src, ""))
d2   = my.dir.create(file.path(src, ""))
d3   = my.dir.create(file.path(d2, "dir3"))
d4   = my.dir.create(file.path(d3, "dir4"))
d5   = my.dir.create(file.path(d4, "dir5@BAR@"))
writeLines(c("File1:", "FOO: @FOO@"),     file.path(d1, ""))
writeLines(c("File2:", "BAR: @BAR@"),     file.path(d2, ""))
writeLines(c("File3:", "SUN: @SUN@"),     file.path(d3, ""))
writeLines(c("File4:", "MOON: @MOON@"),   file.path(d4, "@SUN@.txt"))

## call copySubstitute
copySubstitute(src, dest, recursive=TRUE,
               symbolValues = list(FOO="thefoo", BAR="thebar",
                                   SUN="thesun", MOON="themoon"))

## view the result
listsrc  = dir(src,  full.names=TRUE, recursive=TRUE)
listdest = dir(dest, full.names=TRUE, recursive=TRUE)

cat(unlist(lapply(listsrc,  readLines)), sep="\n")
cat(unlist(lapply(listdest, readLines)), sep="\n")

[Package Biobase version 1.8.0 Index]