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From: Johannes Rainer <johannes.rainer@gmail.com>
To: emacs-orgmode@gnu.org
Subject: org mode R remote code evaluation
Date: Thu, 29 Aug 2013 08:31:15 +0200	[thread overview]
Message-ID: <CABxYo6qtGn_as2mS=Nd86OZQLJgBF_hU+1U_4xT2=y2WGdV91A@mail.gmail.com> (raw)

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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

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next             reply	other threads:[~2013-08-29  6:31 UTC|newest]

Thread overview: 18+ messages / expand[flat|nested]  mbox.gz  Atom feed  top
2013-08-29  6:31 Johannes Rainer [this message]
2013-08-29  8:25 ` org mode R remote code evaluation Loris Bennett
2013-08-29 10:42   ` Johannes Rainer
2013-09-23 16:45     ` Alexander Vorobiev
2013-09-24 12:57       ` Michael Albinus
2013-09-24 13:21         ` Alexander Vorobiev
2013-09-24 13:25           ` Michael Albinus
     [not found]             ` <CAGOCFPUyTaQzVTSwjUOJBfwF8vUzyw=Gn43+bHs8Go8+RUU+nA@mail.gmail.com>
2013-09-24 18:40               ` Michael Albinus
2013-09-25  4:24                 ` Alexander Vorobiev
2013-09-25 10:44                   ` Michael Albinus
2013-09-25 18:15                     ` Eric Schulte
2013-09-25 19:03                       ` Michael Albinus
2013-09-25 20:36                         ` Alexander Vorobiev
2013-09-26  8:11                           ` Michael Albinus
     [not found]                             ` <CAGOCFPXj2-3FruuD=K7=H+SQ308dzkH1P=qP0b17xQuoW9MkPQ@mail.gmail.com>
     [not found]                               ` <87mwmzy16d.fsf@gmx.de>
2013-09-26 17:28                                 ` Alexander Vorobiev
2013-09-26 17:43                                   ` Michael Albinus
2013-09-27 11:39                       ` Michael Albinus
2013-09-28 11:41                         ` Eric Schulte

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