From mboxrd@z Thu Jan 1 00:00:00 1970 From: Johannes Rainer Subject: Re: org mode R remote code evaluation Date: Thu, 29 Aug 2013 12:42:41 +0200 Message-ID: References: <87d2ownbtv.fsf@hornfels.zedat.fu-berlin.de> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary=089e01294a50ee978f04e513c3d2 Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:33255) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VEzgZ-0005We-Ja for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 06:42:45 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1VEzgX-00082w-SP for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 06:42:43 -0400 Received: from mail-ve0-x233.google.com ([2607:f8b0:400c:c01::233]:49878) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1VEzgX-00082o-Lv for emacs-orgmode@gnu.org; Thu, 29 Aug 2013 06:42:41 -0400 Received: by mail-ve0-f179.google.com with SMTP id c13so156511vea.38 for ; Thu, 29 Aug 2013 03:42:41 -0700 (PDT) In-Reply-To: <87d2ownbtv.fsf@hornfels.zedat.fu-berlin.de> 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: Loris Bennett Cc: emacs-orgmode@gnu.org --089e01294a50ee978f04e513c3d2 Content-Type: text/plain; charset=ISO-8859-1 thanks! so the ":results output" does the trick. On Thu, Aug 29, 2013 at 10:25 AM, Loris Bennett wrote: > 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. > > > -- 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 --089e01294a50ee978f04e513c3d2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
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:
Joha= nnes Rainer <johannes.raine= r@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 &quo= t;:dir"
> parameter. so I went on and tried the following (user/server masked):<= br> >
> #+BEGIN_SRC R :dir /xx@xxx:
> =A0 system("hostname")
> #+END_SRC
>
> when I execute it I get the error:
>
> Tramp: Encoding region using function `base64-encode-region'...don= e
> Tramp: Decoding region into remote file
> /ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/T/R-46345BQ= s...done
> byte-code: Couldn't write region to
> `/ssh:xx@xxx:/var/folders/ny/6kbb36310wz2kww8y8ctry600000gn/T/R-46345B= Qs',
> 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= 9;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) :
> =A0 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-g6= fdc23)
>
> 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 Pathophy= siology,
Biocenter, Medical University Innsbruck,
Innrain 80/82 II, 6= 020 Innsbruck, Austria
and
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Au= stria

Tel.:=A0 =A0=A0 +43 (0)512 9003 70961
Email:=A0 johannes.rainer@i-med= .ac.at
=A0 =A0 =A0 =A0 =A0 =A0 johannes.rainer@tcri.at
URL:=A0=A0 http://bioinfo.i-med.ac.at

<= br>
--089e01294a50ee978f04e513c3d2--