use of "input" in system()

On 4/24/2009 10:29 AM, Mike Miller wrote:

First, it looks like there is bug in the documentation...

According to the documentation for system():

http://stat.ethz.ch/R-manual/R-patched/library/base/html/system.html

   input  if a character vector is supplied, this is copied one string per
          line to a temporary file, and the standard input of command is
          redirected to the file

This seems to mean that the standard input of command is redirected 
*from* the file.  From the file, to the command.  Example:

The redirection is done *to* the file handle.  The fact that input is 
read from that handle is a different issue.

Thanks very much for the reply.  After seeing your response, I'm sure the 
document isn't wrong (not a bug) but it is a very terse explanation that I 
think many people will find hard to follow, as I did.

First, a temporary file is created.  Where is it?  What is it called?  If 
the name/location don't matter, does it even matter that a temporary file 
is created?  Is this just info about the internal workings of R that the 
user doesn't need to know?

Then "the standard input of command is redirected to the file".  I think I 
get this now.  I think it means that this is being done behind the scenes:

command < file

Would it help users to tell them that, if that is correct?  It would have 
helped me.  I think this is basically what it is doing:

# For input to the system command we'll need a command and a vector:
command <- "any command string"
v <- c("some", "vector")

# make a temp file:
filename <- tempfile( tmpdir=tempdir() )
write.table(v, file=filename, sep="\n", row.names=FALSE, col.names=FALSE, quote=FALSE)

# Then I think these two system commands do the same thing:

system( paste(command, "<", filename, sep=" ") )

system( command, input=v )

It would be nice if there were more documentation so that I could 
understand this better.  I wasn't understanding why system() hangs 
sometimes as in the simple examples below, but I think I get it now:  The 
stdout goes only to the last command in a string of semi-colon-separated 
commands.  If that's right, it makes sense.

Mike


This works:

system( "cat -", input="foo" )

foo


This hangs until I hit ctrl-c:

system( "cat - ; echo bar", input="foo" )

This works:

system( "echo bar; cat -", input="foo" )

bar
foo


This hangs until I hit ctrl-c:

system( "cat - ; cat -", input="foo" )

Best,
Mike