From: Alexander Vorobiev <alexander.vorobiev@gmail.com>
To: Johannes Rainer <johannes.rainer@i-med.ac.at>
Cc: Loris Bennett <loris.bennett@fu-berlin.de>,
emacs-orgmode <emacs-orgmode@gnu.org>
Subject: Re: org mode R remote code evaluation
Date: Mon, 23 Sep 2013 11:45:38 -0500 [thread overview]
Message-ID: <CAGOCFPVbzESGQoP1+coYBA8xVOYhf8dCWLt+=fjcWORpY5YO2g@mail.gmail.com> (raw)
In-Reply-To: <CABxYo6r+_8wZRj5=uSiPjJHRCrvBd79abRm_jjFbVwnC2EToKQ@mail.gmail.com>
[-- Attachment #1: Type: text/plain, Size: 3468 bytes --]
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.rainer@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.bennett@fu-berlin.de> wrote:
>
>> Johannes Rainer <johannes.rainer@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.rainer@i-med.ac.at
> johannes.rainer@tcri.at
> URL: http://bioinfo.i-med.ac.at
>
>
>
[-- Attachment #2: Type: text/html, Size: 5220 bytes --]
next prev parent reply other threads:[~2013-09-23 16:46 UTC|newest]
Thread overview: 18+ messages / expand[flat|nested] mbox.gz Atom feed top
2013-08-29 6:31 org mode R remote code evaluation Johannes Rainer
2013-08-29 8:25 ` Loris Bennett
2013-08-29 10:42 ` Johannes Rainer
2013-09-23 16:45 ` Alexander Vorobiev [this message]
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
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://www.orgmode.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to='CAGOCFPVbzESGQoP1+coYBA8xVOYhf8dCWLt+=fjcWORpY5YO2g@mail.gmail.com' \
--to=alexander.vorobiev@gmail.com \
--cc=emacs-orgmode@gnu.org \
--cc=johannes.rainer@i-med.ac.at \
--cc=loris.bennett@fu-berlin.de \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).