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

[William Dunlap]

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
VAR=value;exportVAR)
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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