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

[Sarah Goslee]

Actually, here's another possibility:

system('bash -c "source filename"')

On Thu, Dec 20, 2018 at 10:13 AM Sarah Goslee <sarah.goslee using gmail.com> wrote:
>
> Hi,
>
> I can tell you what the problem is:
>
> You're probably running bash at the terminal command line, as I am:
>
> [sarahg using 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 <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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> > https://stat.ethz.ch/mailman/listinfo/r-help
> > 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



-- 
Sarah Goslee (she/her)
http://www.numberwright.com