[R] use of "input" in system()

[Duncan Murdoch]

On 30/04/2009 12:54 PM, Mike Miller wrote:
> On Fri, 24 Apr 2009, Duncan Murdoch wrote:
> 
>> 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?

I'd say the latter.

> 
> 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's not quite correct.  It does the same thing as that does, but it 
doesn't do that:  the < sign is interpreted by the shell to tell it to 
redirect stdin.

   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 )

Those are different on Windows at least.  The first one will probably 
fail, because very few commands other than shells know how to interpret 
"<".  You need the shell to interpret the "<" sign as a signal to 
redirect input.

Check the man page for a description of this on other systems.

Duncan Murdoch

> 
> 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