R: Functions to Manipulate Connections

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"))

    url(description, open = "", blocking = TRUE,
        encoding = getOption("encoding"))

    gzfile(description, open = "", encoding = getOption("encoding"),
           compression = 6)

    bzfile(description, open = "", encoding = getOption("encoding"))

    unz(description, filename, open = "",
        encoding = getOption("encoding"))

    pipe(description, open = "", encoding = getOption("encoding"))

    fifo(description, open = "", blocking = FALSE,
         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 string. A description of the connection: see ‘Details’.
`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.
`filename` | a filename within a zip file.
`host` | character. Host name for port.
`port` | integer. The TCP port number.
`server` | logical. Should the socket be a client or a server?
`con` | a connection.
`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`.

For `file` the description is either a path to the file to be opened or a complete URL, or `""` (the default) or `"stdin"` or `"clipboard"` (see below).

For `url` the description is a complete URL, including scheme (such as `http://`, `ftp://` or `file://`).

For `gzfile` the description is the path to a file that is compressed by `gzip`: it can also opened uncompressed files.

For `bzfile` the description is the path to a file that is compressed by `bzip2`.

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

For `pipe` the description is the command line to be piped to or from (see the Examples).

For `fifo` the description is the path of the fifo.

`file` allows `description="stdin"` to refer to the C-level `stdin` of the process (which need not be connected to anything in a console version or embedded version of R), provided the C99 function `fdopen` is supported on the platform.

`gzfile` and `bzfile` open the actual file in binary mode and so no translations are done if the original file was a text file. (See `gzcon` for a way to add compression to non-file connections such as URLs.)

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. Note that this will happen automatically in due course if there is no R object referring to the connection.

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

If for a `file` or `fifo` connection the description is `""`, the file/fifo is immediately opened (in `"w+"` mode unless `open="w+b"` is specified) and unlinked from the file system. This provides a temporary file/fifo 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. This is then `file:///path/to/file`, where `path/to/file` is relative to `/`. So although the third slash is strictly part of the specification not part of the path, this can be regarded as a way to specify the file ‘/path/to/file’. It is not possible to specify a relative path using a file URL. Also, no attempt is made to decode an encoded URL: call `URLdecode` if necessary.

Note that `https://` connections are not supported.

### 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

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. Not all builds of R support this, and if yours does not, specifying a non-default encoding will give an error when the connection is opened.

Re-encoding only works for connections in text mode.

The encoding `"UCS-2LE"` is treated specially, as it is the appropriate value for Windows ‘Unicode’ text files. If the first two bytes are the Byte Order Mark `0xFFFE` then these are removed as most implementations of `iconv` do not accept BOMs. Note that some implementations will handle BOMs using encoding `"UCS-2"` but many will not.

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.

### 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. The timeout is set at the time the connection is opened (more precisely, when the last connection of that type – `http:`, `ftp:` or socket – was opened).

### Fifos

Fifos default to non-blocking. That follows Svr4 and is 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 mode `"r"` only. This reads the X11 primary selection (see http://standards.freedesktop.org/clipboards-spec/clipboards-latest.txt), which can also be specified as `"X11_primary"` and the secondary selection as `"X11_secondary"`. On most systems the clipboard selection (that used by ‘Copy’ from an ‘Edit’ menu) can be specified as `"X11_clipboard"`.

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

Unix users wishing to write to one of the selections may be able to do so via `xclip` (http://people.debian.org/~kims/xclip/), for example by `pipe("xclip -i", "w")` for the primary selection.

MacOS X users can use `pipe("pbpaste")` and `pipe("pbcopy", "w")` to read from and write to that system's clipboard.

### 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 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.

`gzcon` to wrap gzip (de)compression around a connection.

### 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(zz <- gzfile("ex.gz"))
    close(zz)
    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(zz <- bzfile("ex.bz2")))
    close(zz)
    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-fifo", "w+")
      writeLines("abc", zz)
      print(readLines(zz))
      close(zz)
      unlink("foo-fifo")
    }

    ## 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(stats::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:
    ## Unix examples of use of anonymous fifo
    con <- fifo("")  # file("") would also work
    writeLines(letters, con)
    readLines(con, n=3)
    readLines(con, n=5)
    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"))
    # read a 'Windows Unicode' file including names
    A <- read.table(file("students", encoding="UCS-2LE"))
    ## End(Not run)

[Package base version 2.6.2 Index]