[R] Problem with system() and source on linux

William Dunlap wdunl@p @ending from tibco@com
Thu Dec 20 16:15:02 CET 2018

Isn't 'source' a csh (tcsh, etc.) command?  The sh (bash, etc.) command is
a period, but
you probably will need to use sh constructs in the file (like
instead of csh constructs (like setenv VAR value).

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Thu, Dec 20, 2018 at 7:00 AM Agustin Lobo <aloboaleu using gmail.com> wrote:

> Hi!
> I quite often use system() to run other programs from within R, but
> have just hitted
> a problem:
> For a given program, I need to set up its environment, which I normally do
> with
> source /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
> from the terminal.
> Now, when I try to do the same from within R, I get:
> > system("source /home/alobo/OTB-6.6.0-Linux64/otbenv.profile",
> intern=TRUE)
> sh: 1: source: not found
> Error in system("source /home/alobo/OTB-6.6.0-Linux64/otbenv.profile",  :
>   error in running command
> I need this command to set the environment before I actually run the
> program. My idea was saving a simple script from within R  in which
> the first line would be
> source /home/alobo/OTB-6.6.0-Linux64/otbenv.profile
> and then run the script with system(), but I get that odd error with
> source. I thought source was just
> a plain linux command, how can it be "not found" from within system()?
> Any help much appreciated,
> Thanks
> --
> Agustin Lobo
> aloboaleu using gmail.com
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