The ":results output" doesn't help in my setup (I'm on Windows, the remote
system is linux, access is via putty/plink)
#+BEGIN_SRC sh :results output :dir /grid:
ls
#+END_SRC
executing Sh code block...
Tramp: Encoding region using function `base64-encode-region'...done
Tramp: Decoding region into remote file
/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY...done
byte-code: Couldn't write region to
`/plinkx:grid:/Users/avorobi/AppData/Local/Temp/ob-input-6116fuY', decode
using `tramp_perl_decode_with_module >%s' failed
The /Users directory obviously does not exist on linux.
Tramp itself works in my configuration, I can open files, etc. I have the
latest org-mode from elpa.
Thanks,
Alex
On Thu, Aug 29, 2013 at 5:42 AM, Johannes Rainer <
johannes.rai...@i-med.ac.at> wrote:
> thanks! so the ":results output" does the trick.
>
>
>
>
> On Thu, Aug 29, 2013 at 10:25 AM, Loris Bennett <
> loris.benn...@fu-berlin.de> wrote:
>
>> Johannes Rainer <johannes.rai...@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.rai...@i-med.ac.at
> johannes.rai...@tcri.at
> URL: http://bioinfo.i-med.ac.at
>
>
>
