[R] pipe and binary i/o

Huntsinger, Reid reid_huntsinger at merck.com
Mon Aug 5 21:35:56 CEST 2002

I often want to use "pipe" with "readBin" to read (binary) data from the
standard output of a Perl or C program. For that I need "pipe" to work with
the "open='rb'" option. It never worked for me, and after a look at the
connections.c file, I see that in "pipe_open" the mode gets passed directly
to "popen" (I'm using Linux on an Intel machine). Popen doesn't know "rb"
and fails. I modified the pipe function in connection.c to pass only the
first character of the mode. This seems to work (fingers crossed). Then I
noticed gzfile has the same problem, but bzfile doesn't, and uses the same
solution as I did for pipe. Can I assume that this is a correct fix? Or were
there reasons that pipe and gzfile wouldn't allow "rb"?


Reid Huntsinger

-----Original Message-----
From: Thomas Lumley [mailto:tlumley at u.washington.edu]
Sent: Monday, August 05, 2002 12:17 PM
To: Jim Lemon
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] filename of source file

On Mon, 5 Aug 2002, Jim Lemon wrote:

> David Richmond wrote:
> > Yes, source refers to the use of the source() function. Suppose I invoke
> > a file like so:
> >
> > source("/path/name/filename.r")
> >
> > I want to insert a command in filename.r like so:
> >
> > fullpath <- magic_command()
> >
> > such that fullpath is now "/path/name/filename.r"
> >
> How about
> source(fullpath<-"/path/name/filename.r") ?

That will work only when run at the top level.

If it isn't sufficient to know the directory


in which case magic.command() is getwd(), there isn't a nice way to do it.

Two not-so-nice ways

1) modify source() so it does something like


    magic.command<-function() get(".Last.source.file",envir=.GlobalEnv)

2) Get the file name from the environment inside source

	get("file", parent.frame(n-1)

The problem with the first is that it writes in the global workspace and
that it fails if a source()d file source()s another file before you use

The problem with the second is that it will break if the source() function
renamed or if the name of the variable "file" changes.

You also need to be aware that `file' need not be a filename. It could be
a URL [eg source("http://www.bioconductor.org/getBioC.R") ] or a
connection (either a file connection or some other sort).


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