[R] It is possible to use a Shell command inside a R script?

[Duncan Murdoch]

On 8/24/2007 1:05 PM, Gabor Grothendieck wrote:
> On 8/24/07, Dirk Eddelbuettel <edd at debian.org> wrote:
>> On Fri, Aug 24, 2007 at 10:57:46AM -0400, Duncan Murdoch wrote:
>> > On 8/24/2007 10:33 AM, Dirk Eddelbuettel wrote:
>> >> On Fri, Aug 24, 2007 at 08:32:00AM -0400, Duncan Murdoch wrote:
>> >>> On 8/24/2007 6:58 AM, Ronaldo Reis Junior wrote:
>> >>> > Hi,
>> >>> > > It is possible to use a shell command inside a R script?
>> >>> > > I'm write a R script and I like to put somes shell commands inside to
>> >>> R. > Somethink like: convert fig01.png fig01.xpm or sed ..., etc.
>> >>> The details and available functions depend on the platform, but you want
>> >>> to look at ?system, ?shell, and/or ?shell.exec.  (These all exist in
>> >>> Windows; on Unix-alikes, you probably won't have the latter two.)
>> >> Don't forget pipes. R's ability to consistently work on connections that
>> >> may be local
>> >> files, remotes files, program output, ... is a true treasure (and
>> >> thanks and credits to, I believe, Brian Ripley to make it so).
>> >> Eg you can do this   OD <- read.table(pipe("links -dump
>> >> http://cran.r-project.org/src/contrib/ | awk '/tar.gz/ {print $3, $4}'"),
>> >> header=FALSE, col.names=c("file", "date"))
>> >> to get files and dates of files on CRAN.   As I recall, this also works on
>> >> that other operating system, provided
>> >> you do all the legwork of installing other tools, setting PATHs etc
>> >> to provide what works out of the box on the supposedly unfriendlier OS.
>> >
>> > The pipe command you list doesn't work in Windows.  I'd guess this is
>> > because the pipe syntax "|" within the command is unsupported:  it tries to
>> > execute "links", with the rest of the line passed as arguments.  But I
>> > haven't traced through to check on this.
>>
>> Hm, wishful thinking must have gotten the better of me then. Sorry for
>> spreading misinformation about the capabilities of that other OS.
> 
> This works for me on Windows:
> 
>> tab <- read.table(pipe("lynx --nolist --dump http://cran.r-project.org/src/contrib/ | findstr tar.gz"), as.is = TRUE)

Which R version is that?  It doesn't work for me in Rgui, though it does 
  in Rterm, both R-devel versions.

Duncan Murdoch

>> head(tab[3:5])
>                                V3          V4    V5
> 1             ADaCGH_1.3-1.tar.gz 14-May-2007 12:04
> 2                  AIS_1.0.tar.gz 31-Jul-2007 16:38
> 3             AMORE_0.2-10.tar.gz 11-Apr-2007 10:17
> 4               ARES_1.2-2.tar.gz 19-Mar-2007 20:53
> 5 AcceptanceSampling_0.1-1.tar.gz 07-Jul-2007 20:46
> 6           AdaptFit_0.2-1.tar.gz 04-Aug-2007 09:51