Hi Erin,
On Jul 22, 2009, at 2:16 PM, Erin Hodgess wrote:
Dear R People:
I'm running from R to a grid computer and getting some unusual results
with the system command:
e7 <- system("globus-job-run xxxxx /bin/sh -c 'cd $OSG_APP/
engage;chmod 777 oops'",intern=TRUE)
chmod: changing permissions of `oops': Operation not permitted
e7
character(0)
I xx'ed out the site name. Anyhow, I would expect that the e7 would
contain the warning. Is there any way to have e7 contain the warning
please?
You'll see this call in the "Stdout and stderr" section of ?system:
system("some command 2>&1", intern=TRUE)
The "2>&1" is a command that redirects stderr to stdout, and it seems
that intern=TRUE only captures sdout, so in your case, are you running
to commands at once? I don't know, the command looks weird to me, but
I think the help is suggesting to:
e7 <- system("globus-job-run xxxxx /bin/sh -c 'cd $OSG_APP/
engage;chmod 777 oops' 2>&1",intern=TRUE)
??maybe?? or do you have to add the 2>&1 to each of the separate
commands you're invoking? Play around with that and see.
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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