source Read R Code from a File, a Connection or Expressions

Description

source causes R to accept its input from the named file or URL or connection or expressions directly. Input is read and parsed from that file until the end of the file is reached, then the parsed expressions are evaluated sequentially in the chosen environment.

withAutoprint(exprs) is a wrapper for source(exprs = exprs, ..) with different defaults. Its main purpose is to evaluate and auto-print expressions as if in a toplevel context, e.g, as in the R console.

Usage

source(file, local = FALSE, echo = verbose, print.eval = echo,
       exprs, spaced = use_file,
       verbose = getOption("verbose"),
       prompt.echo = getOption("prompt"),
       max.deparse.length = 150, width.cutoff = 60L,
       deparseCtrl = "showAttributes",
       chdir = FALSE,
       encoding = getOption("encoding"),
       continue.echo = getOption("continue"),
       skip.echo = 0, keep.source = getOption("keep.source"))

withAutoprint(exprs, evaluated = FALSE, local = parent.frame(),
              print. = TRUE, echo = TRUE, max.deparse.length = Inf,
              width.cutoff = max(20, getOption("width")),
              deparseCtrl = c("keepInteger", "showAttributes", "keepNA"),
              ...)

Arguments

file	a connection or a character string giving the pathname of the file or URL to read from. "" indicates the connection stdin().
local	TRUE, FALSE or an environment, determining where the parsed expressions are evaluated. FALSE (the default) corresponds to the user's workspace (the global environment) and TRUE to the environment from which source is called.
echo	logical; if TRUE, each expression is printed after parsing, before evaluation.
print.eval, print.	logical; if TRUE, the result of eval(i) is printed for each expression i; defaults to the value of echo.
exprs	for source() and withAutoprint(*, evaluated=TRUE): instead of specifying file, an expression, call, or list of call's, but not an unevaluated “expression”. for withAutoprint() (with default evaluated=FALSE): one or more unevaluated “expressions”.
evaluated	logical indicating that exprs is passed to source(exprs= *) and hence must be evaluated, i.e., a formal expression, call or list of calls.
spaced	logical indicating if newline (hence empty line) should be printed before each expression (when echo = TRUE).
verbose	if TRUE, more diagnostics (than just echo = TRUE) are printed during parsing and evaluation of input, including extra info for each expression.
prompt.echo	character; gives the prompt to be used if echo = TRUE.
max.deparse.length	integer; is used only if echo is TRUE and gives the maximal number of characters output for the deparse of a single expression.
width.cutoff	integer, passed to deparse() which is used (only) when there are no source references.
deparseCtrl	character vector, passed as control to deparse(), see also .deparseOpts. In R version <= 3.3.x, this was hardcoded to "showAttributes", which is the default currently; deparseCtrl = "all" may be preferable, when strict back compatibility is not of importance.
chdir	logical; if TRUE and file is a pathname, the R working directory is temporarily changed to the directory containing file for evaluating.
encoding	character vector. The encoding(s) to be assumed when file is a character string: see file. A possible value is "unknown" when the encoding is guessed: see the ‘Encodings’ section.
continue.echo	character; gives the prompt to use on continuation lines if echo = TRUE.
skip.echo	integer; how many comment lines at the start of the file to skip if echo = TRUE.
keep.source	logical: should the source formatting be retained when echoing expressions, if possible?
...	(for withAutoprint():) further (non-file related) arguments to be passed to source(.).

Details

Note that running code via source differs in a few respects from entering it at the R command line. Since expressions are not executed at the top level, auto-printing is not done. So you will need to include explicit print calls for things you want to be printed (and remember that this includes plotting by lattice, FAQ Q7.22). Since the complete file is parsed before any of it is run, syntax errors result in none of the code being run. If an error occurs in running a syntactically correct script, anything assigned into the workspace by code that has been run will be kept (just as from the command line), but diagnostic information such as traceback() will contain additional calls to withVisible.

All versions of R accept input from a connection with end of line marked by LF (as used on Unix), CRLF (as used on DOS/Windows) or CR (as used on classic Mac OS) and map this to newline. The final line can be incomplete, that is missing the final end-of-line marker.

If keep.source is true (the default in interactive use), the source of functions is kept so they can be listed exactly as input.

Unlike input from a console, lines in the file or on a connection can contain an unlimited number of characters.

When skip.echo > 0, that many comment lines at the start of the file will not be echoed. This does not affect the execution of the code at all. If there are executable lines within the first skip.echo lines, echoing will start with the first of them.

If echo is true and a deparsed expression exceeds max.deparse.length, that many characters are output followed by .... [TRUNCATED] .

Encodings

By default the input is read and parsed in the current encoding of the R session. This is usually what is required, but occasionally re-encoding is needed, e.g. if a file from a UTF-8-using system is to be read on Windows (or vice versa).

The rest of this paragraph applies if file is an actual filename or URL (and not "" nor a connection). If encoding = "unknown", an attempt is made to guess the encoding: the result of localeToCharset() is used as a guide. If encoding has two or more elements, they are tried in turn until the file/URL can be read without error in the trial encoding. If an actual encoding is specified (rather than the default or "unknown") in a Latin-1 or UTF-8 locale then character strings in the result will be translated to the current encoding and marked as such (see Encoding).

If file is a connection (including one specified by ""), it is not possible to re-encode the input inside source, and so the encoding argument is just used to mark character strings in the parsed input in Latin-1 and UTF-8 locales: see parse.

References

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.

See Also

demo which uses source; eval, parse and scan; options("keep.source").

sys.source which is a streamlined version to source a file into an environment.

‘The R Language Definition’ for a discussion of source directives.

Examples

someCond <- 7 > 6
## want an if-clause to behave "as top level" wrt auto-printing :
## (all should look "as if on top level", e.g. non-assignments should print:)
if(someCond) withAutoprint({
   x <- 1:12
   x-1
   (y <- (x-5)^2)
   z <- y
   z - 10
})

## If you want to source() a bunch of files, something like
## the following may be useful:
 sourceDir <- function(path, trace = TRUE, ...) {
    op <- options(); on.exit(options(op)) # to reset after each 
    for (nm in list.files(path, pattern = "[.][RrSsQq]$")) {
       if(trace) cat(nm,":")
       source(file.path(path, nm), ...)
       if(trace) cat("\n")
       options(op)
    }
 }

suppressWarnings( rm(x,y) ) # remove 'x' or 'y' from global env
withAutoprint({ x <- 1:2; cat("x=",x,"\n"); y <- x^2 })
## x and y now exist:
stopifnot(identical(x, 1:2), identical(y, x^2))

withAutoprint({ formals(sourceDir); body(sourceDir) },
              max.deparse.length = 20, verbose = TRUE)