Hi,
I can tell you what the problem is:
You're probably running bash at the terminal command line, as I am:
[sarahg@localhost]$ echo $0
bash
but the R system function uses sh
> system("echo $0")
sh
The bash shell has a source command; the sh shell doesn't. See here
for a possible solution:
https://stackoverflow.com/questions/4732200/replacement-for-source-in-sh
I don't know if there's a way to specify bash shell in system(); a
very cursory googling didn't find anything. If you find a way, please
report back.
Sarah
On Thu, Dec 20, 2018 at 10:00 AM Agustin Lobo <aloboa...@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
> aloboa...@gmail.com
>
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
--
Sarah Goslee (she/her)
http://www.numberwright.com
______________________________________________
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