From mboxrd@z Thu Jan 1 00:00:00 1970 From: Johannes Rainer Subject: org mode R remote code evaluation Date: Thu, 29 Aug 2013 08:31:15 +0200 Message-ID: Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=047d7b675818c22f3004e51040a6 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:40010) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VEvlK-0007of-SY for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 02:31:23 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VEvlG-0004eS-3X for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 02:31:22 -0400 Received: from mail-qa0-x22c.google.com ([2607:f8b0:400d:c00::22c]:64629) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VEvlF-0004eJ-W5 for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 02:31:18 -0400 Received: by mail-qa0-f44.google.com with SMTP id w8so2806522qac.17 for ; Wed, 28 Aug 2013 23:31:17 -0700 (PDT) List-Id: "General discussions about Org-mode." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org Sender: emacs-orgmode-bounces+geo-emacs-orgmode=m.gmane.org@gnu.org To: emacs-orgmode@gnu.org --047d7b675818c22f3004e51040a6 Content-Type: text/plain; charset=ISO-8859-1 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 --047d7b675818c22f3004e51040a6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
dear all,

I have some computat= ion 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" parame= ter. so I went on and tried the following (user/server masked):

#+BEGIN_SRC R :dir /xx@xxx:
=A0 system("hostname")
#+EN= D_SRC

when I execute it I get the error:

Tramp: Encodin= g region using function `base64-encode-region'...done
Tramp: Decodin= g region into remote file /ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctr= y600000gn/T/R-46345BQs...done
byte-code: Couldn't write region to `/ssh:xx@xxx:/var/folders/ny/6kbb36= 310wz2kww8y8ctry600000gn/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 a= lso tried to start a ssh session using "M-x ssh" and used the sou= rce block

#+BEGIN_SRC R :exports both :session *ssh xxx*
system("hostname= ")
#+END_SRC

on the server it executes the comman= d but it can not write the results:

> xxx
> Warning message= :
In file.rename(tfile, transfer.file) :
=A0 cannot rename file '/tmp/= RtmpsirjGl/file51c8f6ce4ec' to '/var/folders/ny/6kbb36310wz2kww8y8c= try600000gn/T/babel-46345zSH/R-46345a4N', reason 'No such file or d= irectory'
>

I am using emacs 24.3 and Org-mode versio= n 8.0.7 (release_8.0.7-384-g6fdc23)

I would be helpful fo= r any suggestions how I could solve this problem.

thanks = in advance
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