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