From mboxrd@z Thu Jan 1 00:00:00 1970 From: "Loris Bennett" Subject: Re: org mode R remote code evaluation Date: Thu, 29 Aug 2013 10:25:00 +0200 Message-ID: <87d2ownbtv.fsf@hornfels.zedat.fu-berlin.de> References: Mime-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:34048) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VExXZ-0005Uo-LB for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 04:25:33 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VExXS-0005VM-8k for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 04:25:17 -0400 Received: from plane.gmane.org ([80.91.229.3]:44875) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VExXS-0005VA-0G for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 04:25:10 -0400 Received: from list by plane.gmane.org with local (Exim 4.69) (envelope-from ) id 1VExXQ-0003NW-NM for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 10:25:08 +0200 Received: from hornfels.zedat.fu-berlin.de ([160.45.11.110]) by main.gmane.org with esmtp (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Thu, 29 Aug 2013 10:25:08 +0200 Received: from loris.bennett by hornfels.zedat.fu-berlin.de with local (Gmexim 0.1 (Debian)) id 1AlnuQ-0007hv-00 for ; Thu, 29 Aug 2013 10:25:08 +0200 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 Johannes Rainer 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.