connections: Functions to Manipulate Connections (Files, URLs, ...)

In robertzk/monadicbase: The R Base Package

Description

Functions to create, open and close connections, i.e., “generalized files”, such as possibly compressed files, URLs, pipes, etc.

Usage

file(description = "", open = "", blocking = TRUE,
     encoding = getOption("encoding"), raw = FALSE,
     method = getOption("url.method", "default"))

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

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

bzfile(description, open = "", encoding = getOption("encoding"),
       compression = 9)

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

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"),
                 timeout = getOption("timeout"))

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 string. A description of how to open the connection (if it should be opened initially). See section ‘Modes’ for possible values.
blocking	logical. See the ‘Blocking’ section.
encoding	The name of the encoding to be assumed. See the ‘Encoding’ section.
raw	logical. If true, a ‘raw’ interface is used which will be more suitable for arguments which are not regular files, e.g. character devices. This suppresses the check for a compressed file when opening for text-mode reading, and asserts that the ‘file’ may not be seekable.
method	character string, partially matched to c("default", "internal", "wininet", "libcurl"): see ‘Details’.
compression	integer in 0–9. The amount of compression to be applied when writing, from none to maximal available. For xzfile can also be negative: see the ‘Compression’ section.
timeout	numeric: the timeout (in seconds) to be used for this connection. Beware that some OSes may treat very large values as zero: however the POSIX standard requires values up to 31 days to be supported.
filename	a filename within a zip file.
host	character string. Host name for the port.
port	integer. The TCP port number.
server	logical. Should the socket be a client or a server?
con	a connection.
type	character string. Currently ignored.
rw	character string. Empty or "read" or "write", partial matches allowed.
...	arguments passed to or from other methods.

Details

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

For file the description is a path to the file to be opened or a complete URL (when it is the same as calling url), or "" (the default) or "clipboard" (see the ‘Clipboard’ section). Use "stdin" to refer to the C-level ‘standard input’ of the process (which need not be connected to anything in a console or embedded version of R, and is not in RGui on Windows). See also stdin() for the subtly different R-level concept of stdin.

For url the description is a complete URL including scheme (such as http://, https://, ftp:// or file://). Method "internal" is that available since connections were introduced, method "wininet" is only available on Windows (it uses the WinInet functions of that OS) and method "libcurl" (using the library of that name: http://curl.haxx.se/libcurl/) is required on a Unix-alike but optional on Windows. Method "default" uses method "internal" for file: URLs and "libcurl" for ftps: URLs. On a Unix-alike it uses "internal" for http: and ftp: URLs and "libcurl" for https: URLs; on Windows "wininet" for http:, ftp: and https: URLs. Proxies can be specified: see download.file.

For gzfile the description is the path to a file compressed by gzip: it can also open for reading uncompressed files and those compressed by bzip2, xz or lzma.

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

For xzfile the description is the path to a file compressed by xz (https://en.wikipedia.org/wiki/Xz) or (for reading only) lzma (https://en.wikipedia.org/wiki/LZMA).

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. This is run in a shell, on Windows that specified by the COMSPEC environment variable.

For fifo the description is the path of the fifo. (Support for fifo connections is optional but they are available on most Unix platforms and on Windows.)

The intention is that file and gzfile can be used generally for text input (from files, http:// and https:// URLs) and binary input respectively.

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.

close closes and destroys a connection. This will happen automatically in due course (with a warning) if there is no longer an R object referring to the connection.

A maximum of 128 connections can be allocated (not necessarily open) at any one time. Three of these are pre-allocated (see stdout). The OS will impose limits on the numbers of connections of various types, but these are usually larger than 125.

flush flushes the output stream of a connection open for write/append (where implemented, currently for file and clipboard connections, stdout and stderr).

If for a file or (on most platforms) a 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.

Value

file, pipe, fifo, url, gzfile, bzfile, xzfile, unz and socketConnection return a connection object which inherits from class "connection" and has a first more specific class.

open and flush return NULL, invisibly.

close returns either NULL or an integer status, invisibly. The status is from when the connection was last closed and is available only for some types of connections (e.g., pipes, files and fifos): typically zero values indicate success.

isOpen returns a logical value, whether the connection is currently open.

isIncomplete returns a logical value, whether the last read attempt was blocked, or for an output text connection whether there is unflushed output.

URLs

url and file support URL schemes file://, http://, https:// and ftp://.

method = "libcurl" allows more schemes: exactly which schemes is platform-dependent (see libcurlVersion), but all Unix-alike platforms will support https:// and most platforms will support ftps://.

Most methods do not percent-encode special characters such as spaces in http:// URLs (see URLencode), but it seems the "wininet" method does.

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.

On a Unix-alike, 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.

In this form the path is relative to the root of the filesystem, not a Windows concept. The standard form on Windows is file:///d:/R/repos: for compatibility with earlier versions of R and Unix versions, any other form is parsed as R as file:// plus path_to_file. Also, backslashes are accepted within the path even though RFC1738 does not allow them.

No attempt is made to decode a percent-encoded file: URL: call URLdecode if necessary.

The "internal" method does not follow re-directed HTTP URLs: both methods "wininet" (the default on Windows) and "libcurl" do (including for HTTPS URLs).

Server-side cached data is always accepted.

Function download.file and contributed package RCurl provide more comprehensive facilities to download from URLs.

Modes

Possible values for the argument open 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 both reading and writing. An unsupported mode is usually silently substituted.

If a file or fifo is created on a Unix-alike, its permissions will be the maximal allowed by the current setting of umask (see Sys.umask).

For many connections there is little or no difference between text and binary modes. For file-like connections on Windows, translation of line endings (between LF and CRLF) is done in text mode only (but text read operations on connections such as readLines, scan and source work for any form of line ending). Various R operations are possible in only one of the modes: for example pushBack is text-oriented and is only allowed on connections open for reading in text mode, and binary operations such as readBin, load and save can only be done on binary-mode connections.

The mode of a connection is determined when actually opened, which is deferred if open = "" is given (the default for all but socket connections). An explicit call to open can specify the mode, but otherwise the mode will be "r". (gzfile, bzfile and xzfile connections are exceptions, as the compressed file always has to be opened in binary mode and no conversion of line-endings is done even on Windows, so the default mode is interpreted as "rb".) Most operations that need write access or text-only or binary-only mode will override the default mode of a non-yet-open connection.

Append modes need to be considered carefully for compressed-file connections. They do not produce a single compressed stream on the file, but rather append a new compressed stream to the file. Readers may or may not read beyond end of the first stream: currently R does so for gzfile, bzfile and xzfile connections.

Compression

R supports gzip, bzip2 and xz compression (added in R 2.10.0: also read-only support for its precursor lzma compression).

For reading, the type of compression (if any) can be determined from the first few bytes of the file. Thus for file(raw = FALSE) connections, if open is "", "r" or "rt" the connection can read any of the compressed file types as well as uncompressed files. (Using "rb" will allow compressed files to be read byte-by-byte.) Similarly, gzfile connections can read any of the forms of compression and uncompressed files in any read mode.

(The type of compression is determined when the connection is created if open is unspecified and a file of that name exists. If the intention is to open the connection to write a file with a different form of compression under that name, specify open = "w" when the connection is created or unlink the file before creating the connection.)

For write-mode connections, compress specifies how hard the compressor works to minimize the file size, and higher values need more CPU time and more working memory (up to ca 800Mb for xzfile(compress = 9)). For xzfile negative values of compress correspond to adding the xz argument -e: this takes more time (double?) to compress but may achieve (slightly) better compression. The default (6) has good compression and modest (100Mb memory) usage: but if you are using xz compression you are probably looking for high compression.

Choosing the type of compression involves tradeoffs: gzip, bzip2 and xz are successively less widely supported, need more resources for both compression and decompression, and achieve more compression (although individual files may buck the general trend). Typical experience is that bzip2 compression is 15% better on text files than gzip compression, and xz with maximal compression 30% better. The experience with R save files is similar, but on some large ‘.rda’ files xz compression is much better than the other two. With current computers decompression times even with compress = 9 are typically modest and reading compressed files is usually faster than uncompressed ones because of the reduction in disc activity.

Encoding

The encoding of the input/output stream of a connection 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 encoding 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: reading from a connection with re-encoding specified in binary mode will read the stream of bytes, but mixing text and binary mode reads (e.g., mixing calls to readLines and readChar) is likely to lead to incorrect results.

The encodings "UCS-2LE" and "UTF-16LE" are treated specially, as they are appropriate values for Windows ‘Unicode’ text files. If the first two bytes are the Byte Order Mark 0xFEFF then these are removed as some implementations of iconv do not accept BOMs. Note that whereas most implementations will handle BOMs using encoding "UCS-2" and choose the appropriate byte order, some (including earlier versions of glibc) will not. There is a subtle distinction between "UTF-16" and "UCS-2" (see https://en.wikipedia.org/wiki/UTF-16: the use of characters in the ‘Supplementary Planes’ which need surrogate pairs is very rare so "UCS-2LE" is an appropriate first choice (as it is more widely implemented).

As from R 3.0.0 the encoding "UTF-8-BOM" is accepted for reading and will remove a Byte Order Mark if present (which it often is for files and webpages generated by Microsoft applications). If a BOM is required (it is not recommended) when writing it should be written explicitly, e.g. by writeChar("\ufeff", con, eos = NULL) or writeBin(as.raw(c(0xef, 0xbb, 0xbf)), binary_con)

Encoding names "utf8", "mac" and "macroman" are not portable, and not supported on all current R platforms. "UTF-8" is portable and "macintosh" is the official (and most widely supported) name for ‘Mac Roman’.

Requesting a conversion that is not supported is an error, reported when the connection is opened. Exactly what happens when the requested translation cannot be done for invalid input is in general undocumented. 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.

It may be possible to deduce the current native encoding from Sys.getlocale("LC_CTYPE"), but not all OSes record it.

Blocking

Whether or not the connection blocks can be specified for file, url (default yes), fifo and socket connections (default not).

In blocking mode, functions using the connection do not return to the R evaluator until the read/write is 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 R process will be blocked during a DNS lookup on Unix, for example.

Most blocking operations on HTTP/FTP URLs and on sockets are subject to the timeout set by options("timeout"). Note that this is a timeout for no response, 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 S version 4 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 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 X11 selections may be able to do so via xclip (http://sourceforge.net/projects/xclip/) or xsel (http://www.vergenet.net/~conrad/software/xsel/), for example by pipe("xclip -i", "w") for the primary selection.

OS 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 S model, for example in output text connections and URL, compressed and socket connections.

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

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

References

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

Ripley, B. D. (2001) Connections. R News, 1/1, 16–7. https://www.r-project.org/doc/Rnews/Rnews_2001-1.pdf

See Also

textConnection, seek, showConnections, pushBack.

Functions making direct use of connections are (text-mode) readLines, writeLines, cat, sink, scan, parse, read.dcf, dput, dump and (binary-mode) readBin, readChar, writeBin, writeChar, load and save.

capabilities to see if fifo connections are supported by this build of R.

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

options HTTPUserAgent, internet.info and timeout are used by some of the methods for URL connections.

memCompress for more ways to (de)compress and references on data compression.

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)

## Not run: ## fifo example -- may hang even with OS support for fifos
if(capabilities("fifo")) {
  zz <- fifo("foo-fifo", "w+")
  writeLines("abc", zz)
  print(readLines(zz))
  close(zz)
  unlink("foo-fifo")
}
## End(Not run)

## Unix examples of use of pipes

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

# remove trailing commas.  Suppose

## Not run: % 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
## End(Not run)
# Then read this by
scan(pipe("sed -e s/,$// data2_"), sep = ",")


# convert decimal point to comma in output: see also write.table
# both R strings and (probably) the shell need \ doubled
zz <- pipe(paste("sed s/\\\\./,/ >", "outfile"), "w")
cat(format(round(stats::rnorm(48), 4)), fill = 70, file = zz)
close(zz)
file.show("outfile", delete.file = TRUE)

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

con <- socketConnection(port = 79, blocking = TRUE)
writeLines(paste0(system("whoami", intern = TRUE), "\r"), 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)
   z <- readLines(con2)
   if(length(z)) print(z)
}
close(con2)

## examples of use of encodings
# write a file in UTF-8
cat(x, file = (con <- file("foo", "w", encoding = "UTF-8"))); close(con)
# read a 'Windows Unicode' file
A <- read.table(con <- file("students", encoding = "UCS-2LE")); close(con)

## End(Not run)

robertzk/monadicbase documentation built on May 27, 2019, 10:35 a.m.