thanks! so the ":results output" does the trick.




On Thu, Aug 29, 2013 at 10:25 AM, Loris Bennett
<loris.bennett@fu-berlin.de>wrote:

> Johannes Rainer <johannes.rainer@gmail.com> writes:
>
> > dear all,
> >
> > I have some computation intense R-code that I want to run remotely on my
> server,
> > and, according to the org manual that should be possible with the ":dir"
> > parameter. so I went on and tried the following (user/server masked):
> >
> > #+BEGIN_SRC R :dir /xx@xxx:
> >   system("hostname")
> > #+END_SRC
> >
> > when I execute it I get the error:
> >
> > Tramp: Encoding region using function `base64-encode-region'...done
> > Tramp: Decoding region into remote file
> > /ssh:xx@xxx
> :/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/T/R-46345BQs...done
> > byte-code: Couldn't write region to
> > `/ssh:xx@xxx
> :/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/T/R-46345BQs',
> > decode using `base64 -d -i >%s' failed
> >
> > apparently, this temp folder does not exist on the linux server, it is
> actually
> > the temp folder from my local machine.
> >
> > I get the same error when I try to execute remote shell code, so it's
> not R
> > related.
> >
> > I also tried to start a ssh session using "M-x ssh" and used the source
> block
> >
> > #+BEGIN_SRC R :exports both :session *ssh xxx*
> > system("hostname")
> > #+END_SRC
> >
> > on the server it executes the command but it can not write the results:
> >
> >> xxx
> >> Warning message:
> > In file.rename(tfile, transfer.file) :
> >   cannot rename file '/tmp/RtmpsirjGl/file51c8f6ce4ec' to
> >
> '/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/T/babel-46345zSH/R-46345a4N',
> > reason 'No such file or directory'
> >>
> >
> > I am using emacs 24.3 and Org-mode version 8.0.7
> (release_8.0.7-384-g6fdc23)
> >
> > I would be helpful for any suggestions how I could solve this problem.
> >
> > thanks in advance
>
> The following works for me:
>
> #+BEGIN_SRC R :results output :dir /xxx@xxxxx:
> system("hostname")
> #+END_SRC
>
> with Emacs 24.2.1 and 8.0.7 (8.0.7-6-g13cb28-elpaplus)
>
> Cheers,
>
> Loris
>
> --
> This signature is currently under construction.
>
>
>


-- 
Johannes Rainer, PhD
Applied Bioinformatics Group,
Division Molecular Pathophysiology,
Biocenter, Medical University Innsbruck,
Innrain 80/82 II, 6020 Innsbruck, Austria
and
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria

Tel.:     +43 (0)512 9003 70961
Email:  johannes.rainer@i-med.ac.at
            johannes.rainer@tcri.at
URL:   http://bioinfo.i-med.ac.at