connections {base}R Documentation

Functions to Manipulate Connections

Description

Functions to create, open and close connections.

Usage

file(description = "", open = "", blocking = TRUE,
     encoding = getOption("encoding"))
pipe(description, open = "", encoding = getOption("encoding"))
fifo(description = "", open = "", blocking = FALSE,
     encoding = getOption("encoding"))
gzfile(description, open = "", encoding = getOption("encoding"),
       compression = 6)
unz(description, filename, open = "", encoding = getOption("encoding"))
bzfile(description, open = "", encoding = getOption("encoding"))
url(description, open = "", blocking = TRUE,
    encoding = getOption("encoding"))
socketConnection(host = "localhost", port, server = FALSE,
                 blocking = FALSE, open = "a+",
                 encoding = getOption("encoding"))

open(con, ...)
## S3 method for class 'connection':
open(con, open = "r", blocking = TRUE, ...)

close(con, ...)
## S3 method for class 'connection':
close(con, type = "rw", ...)

flush(con)

isOpen(con, rw = "")
isIncomplete(con)

Arguments

description character. A description of the connection. For file and pipe this is a path to the file to be opened. For url it is a complete URL, including schemes (http://, ftp:// or file:// – see Details). file also accepts complete URLs.
filename a filename within a zip file.
con a connection.
host character. Host name for port.
port integer. The TCP port number.
server logical. Should the socket be a client or a server?
open character. A description of how to open the connection (if at all). See Details for possible values.
blocking logical. See the ‘Blocking’ section below.
encoding The name of the encoding to be used. See the ‘Encoding’ section below.
compression integer in 0–9. The amount of compression to be applied when writing, from none to maximal. The default is a good space/time compromise.
type character. Currently ignored.
rw character. Empty or "read" or "write", partial matches allowed.
... arguments passed to or from other methods.

Details

The first eight functions create connections. By default the connection is not opened (except for socketConnection), but may be opened by setting a non-empty value of argument open.

gzfile applies to files compressed by ‘gzip’, and bzfile to those compressed by ‘bzip2’: such connections can only be binary.

unz reads (only) single files within zip files, in binary mode. The description is the full path, with ‘.zip’ extension if required.

All platforms support file, gzfile, bzfile, unz and url("file://") connections. The other types may be partially implemented or not implemented at all. (They do work on most Unix platforms, and all but fifo on Windows.)

Proxies can be specified for url connections: see download.file.

open, close and seek are generic functions: the following applies to the methods relevant to connections.

open opens a connection. In general functions using connections will open them if they are not open, but then close them again, so to leave a connection open call open explicitly.

Possible values for the mode open to open a connection are

"r" or "rt"
Open for reading in text mode.
"w" or "wt"
Open for writing in text mode.
"a" or "at"
Open for appending in text mode.
"rb"
Open for reading in binary mode.
"wb"
Open for writing in binary mode.
"ab"
Open for appending in binary mode.
"r+", "r+b"
Open for reading and writing.
"w+", "w+b"
Open for reading and writing, truncating file initially.
"a+", "a+b"
Open for reading and appending.

Not all modes are applicable to all connections: for example URLs can only be opened for reading. Only file and socket connections can be opened for reading and writing/appending. For many connections there is little or no difference between text and binary modes, but there is for file-like connections on Windows, and pushBack is text-oriented and is only allowed on connections open for reading in text mode.

close closes and destroys a connection.

flush flushes the output stream of a connection open for write/append (where implemented).

If for a file connection the description is "", the file is immediately opened (in "w+" mode unless open="w+b" is specified) and unlinked from the file system. This provides a temporary file to write to and then read from.

A note on file:// URLs. The most general form (from RFC1738) is file://host/path/to/file, but R only accepts the form with an empty host field referring to the local machine. In this form the path is relative to the root of the filesystem, not a Windows concept. So this is parsed in R as file:// plus /path/to/file, e.g. file:///TEMP/some (referring to the current drive) or file://d:/R/repos. Note that although most browsers will accept these forms, strictly there should be three initial slashes in the second (but not four in the first) and R does not accept that form. Also, backslashes are accepted within the path even though RFC1738 does not allow them.

Value

file, pipe, fifo, url, gzfile, bzfile, unz and socketConnection return a connection object which inherits from class "connection" and has a first more specific class.
isOpen returns a logical value, whether the connection is currently open.
isIncomplete returns a logical value, whether last read attempt was blocked, or for an output text connection whether there is unflushed output.

Encoding

Note: prior to R 2.1.0 there was a byte-by-byte encoding option applied to input only. This has been replaced by a more comprehensive scheme.

The encoding of the input/output stream of a connection in text mode can be specified by name, in the same way as it would be given to iconv: see that help page for how to find out what names are recognized on your platform. Additionally, "" and "native.enc" both mean the ‘native’ encoding, that is the internal encoding of the current locale and hence no translation is done.

Re-encoding only works for connections in text mode.

Exactly what happens when the requested translation cannot be done is in general undocumented. Requesting a conversion that is not supported is an error, reported when the connection is opened. On output the result is likely to be that up to the error, with a warning. On input, it will most likely be all or some of the input up to the error.

The encoding for stdin when redirected from a file can be set by the command-line flag --encoding.

Blocking

The default condition for all but fifo and socket connections is to be in blocking mode. In that mode, functions do not return to the R evaluator until they are complete. In non-blocking mode, operations return as soon as possible, so on input they will return with whatever input is available (possibly none) and for output they will return whether or not the write succeeded.

The function readLines behaves differently in respect of incomplete last lines in the two modes: see its help page.

Even when a connection is in blocking mode, attempts are made to ensure that it does not block the event loop and hence the operation of GUI parts of R. These do not always succeed, and the whole process will be blocked during a DNS lookup on Unix, for example.

Most blocking operations on URLs and sockets are subject to the timeout set by options("timeout"). Note that this is a timeout for no response at all, not for the whole operation.

Fifos

Fifos default to non-blocking. That follows Svr4 and it probably most natural, but it does have some implications. In particular, opening a non-blocking fifo connection for writing (only) will fail unless some other process is reading on the fifo.

Opening a fifo for both reading and writing (in any mode: one can only append to fifos) connects both sides of the fifo to the R process, and provides an similar facility to file().

Clipboard

file can also be used with description = "clipboard" in modes "r" and "w" only.

When the clipboard is opened for reading, the contents are immediately copied to internal storage in the connection.

When writing to the clipboard, the output is copied to the clipboard only when the connection is closed or flushed. There is a 32Kb limit on the text to be written to the clipboard. This can be raised by using e.g. file("clipboard-128") on NT-based versions of Windows, to give 128Kb.

At least on NT-based versions of Windows the clipboard works in Unicode wide characters, so encodings are likely not to work as one might expect.

Note

R's connections are modelled on those in S version 4 (see Chambers, 1998). However R goes well beyond the Svr4 model, for example in output text connections and URL, gzfile, bzfile and socket connections.

The default mode in R is "r" except for socket connections. This differs from Svr4, where it is the equivalent of "r+", known as "*".

On platforms where vsnprintf does not return the needed length of output (e.g., Windows) there is a 100,000 character output limit on the length of line for fifo, gzfile and bzfile connections: longer lines will be truncated with a warning.

References

Chambers, J. M. (1998) Programming with Data. A Guide to the S Language. Springer.

See Also

textConnection, seek, readLines, readBin, writeLines, writeBin, showConnections, pushBack.

capabilities to see if url, fifo and socketConnection are supported by this build of R.

To flush output to the console, see flush.console.

Examples

zz <- file("ex.data", "w")  # open an output file connection
cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n")
cat("One more line\n", file = zz)
close(zz)
readLines("ex.data")
unlink("ex.data")

zz <- gzfile("ex.gz", "w")  # compressed file
cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n")
close(zz)
readLines(gzfile("ex.gz"))
unlink("ex.gz")

zz <- bzfile("ex.bz2", "w")  # bzip2-ed file
cat("TITLE extra line", "2 3 5 7", "", "11 13 17", file = zz, sep = "\n")
close(zz)
print(readLines(bzfile("ex.bz2")))
unlink("ex.bz2")

## An example of a file open for reading and writing
Tfile <- file("test1", "w+")
c(isOpen(Tfile, "r"), isOpen(Tfile, "w")) # both TRUE
cat("abc\ndef\n", file=Tfile)
readLines(Tfile)
seek(Tfile, 0, rw="r") # reset to beginning
readLines(Tfile)
cat("ghi\n", file=Tfile)
readLines(Tfile)
close(Tfile)
unlink("test1")

## We can do the same thing with an anonymous file.
Tfile <- file()
cat("abc\ndef\n", file=Tfile)
readLines(Tfile)
close(Tfile)

if(capabilities("fifo")) {
  zz <- fifo("foo", "w+")
  writeLines("abc", zz)
  print(readLines(zz))
  close(zz)
  unlink("foo")
}

## Not run: ## Unix examples of use of pipes

# read listing of current directory
readLines(pipe("ls -1"))

# remove trailing commas. Suppose
% cat data2
450, 390, 467, 654,  30, 542, 334, 432, 421,
357, 497, 493, 550, 549, 467, 575, 578, 342,
446, 547, 534, 495, 979, 479
# Then read this by
scan(pipe("sed -e s/,$// data2"), sep=",")

# convert decimal point to comma in output
# both R strings and (probably) the shell need \ doubled
zz <- pipe(paste("sed s/\\\\./,/ >", "outfile"), "w")
cat(format(round(rnorm(100), 4)), sep = "\n", file = zz)
close(zz)
file.show("outfile", delete.file=TRUE)## End(Not run)

## Not run: ## example for Unix machine running a finger daemon

con <- socketConnection(port = 79, blocking = TRUE)
writeLines(paste(system("whoami", intern=TRUE), "\r", sep=""), con)
gsub(" *$", "", readLines(con))
close(con)## End(Not run)

## Not run: ## two R processes communicating via non-blocking sockets
# R process 1
con1 <- socketConnection(port = 6011, server=TRUE)
writeLines(LETTERS, con1)
close(con1)

# R process 2
con2 <- socketConnection(Sys.info()["nodename"], port = 6011)
# as non-blocking, may need to loop for input
readLines(con2)
while(isIncomplete(con2)) {Sys.sleep(1); readLines(con2)}
close(con2)
## End(Not run)

## Not run: 
 ## examples of use of encodings
cat(x, file = file("foo", "w", encoding="UTF-8"))
## End(Not run)

[Package base version 2.1.0 Index]